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Danzo Shimura. While he may not have been inflated to insane levels of power like Madara or Obito, or be tied into the deeper history of the world (or classic literature) like Kaguya, he is still one of the biggest antagonists in the series. His actions have caused much of the suffering that went on in Naruto's plot. I've already looked at Hiruzen in the last part of this series, so now, let's take a look at Danzo, and by extension, Root.

Spoilers, both need serious work.

First, let's go over the basics of who Danzo is.

Danzo: A Personality Overview

Danzo is described as an extremist and a war hawk, and that's pretty accurate. He's also a man that believes in the idea of "the ends justify the means." He's the kind of person that will resort to fighting over diplomacy. In fact, I don't think the word diplomacy is even in his vocabulary.

In certain ways, when I look at Danzo and his philosophies, I get the feeling that his mindset is still in the Warring States Period, where all enemies must be conquered. He believes his underhanded actions are necessary and that the village wouldn't survive without him. His father and grandfather, both of whom died in battle, also apparently instilled the importance of self-sacrifice in him, but he has never followed up on it.

Danzo is a hypocrite in that regard. He talks about self-sacrifice and expects his agents to throw away their lives, but he is absolutely unwilling to do so. This also ties back to why he wasn't named Hokage. Remember the old test of character given by Tobirama? Danzo thought about volunteering, but hesitated, and Hiruzen ultimately volunteered before he did.

Ego, I think, is a good way to look at the motivations of a character like Danzo. Many of the villains in Naruto, such as Nagato, Obito, and Madara, are motivated to seek peace because of tragedy. When it comes to Danzo, we don't really know of any tragedy. The character speaks of "bringing peace," but his version of peace is "conquer everybody and put yourself on top."

He believes the Leaf is the village most suited to rule over everyone else. More specifically, he believes that he is suited to rule over everyone else, that his philosophies are the right ones and he knows best and everyone should just do as he says. Nagato may have talked a bit about becoming a god that would bring peace, but it was never based in this level of egotism.

This ego, combined with cowardice, is one reason why Danzo doesn't want to die. He feels he's the only person who can bring about "peace." He did apparently get over his fear at the very end when he tried to take out Sasuke, but personally, a part of me finds it hard to believe a man so convinced of his own importance would ever be able to do that.

Danzo has also commented on emotion. He himself is described as a person who operates on cold, ruthless logic, and at the end of the Tenchi Bridge arc (Full canon, and Shippuden episode 33-53), Danzo tells Sai not to give into emotion, as that leads to hatred which leads to conflict. Root agents are also supposed to discard their emotions.

Danzo despises the ideals of the First Hokage and the Third Hokage. He also despises Tsunade for being the granddaughter of the former and student of the latter. I guess both of them were too ethical for Danzo's taste.

Danzo has also been described as paranoid and not trusting at all, willing to betray Orochimaru in a plan (or perhaps a lie?) to take over the Leaf, realizing that the latter would eventually betray him, despite how much the two had worked together before. He's also been described by many as power hungry, which is rather accurate, what with the way he went after the Sharingan and Hashirama's Wood Style.

Manga Danzo vs. Anime Danzo: Levels of Extremism

One thing that I think should be made clear is that there's a difference, if slight, between the manga version of this character, and the anime version. I know that the Naruto anime is very faithful adaptation of the manga, and that it's filler arcs were often just to pad time or milk the series. I also know that Narutopedia does not distinguish very strongly between the anime and manga. But where Danzo is concerned, there's a difference. He's supposed to be a well-intentioned extremist, but one crosses a line the other won't.

As an example from a completely different fandom, I'd like to direct your attention to the DC Comics character Atrocitus, the leader of the Red Lanterns. They run on the power of rage and hatred (Sasuke would have great qualifications). Atrocitus created this group of literal berserkers after his planet, his whole space sector (there are only 3600 of them, so that gives you a sense of scale), was slaughtered.

This character also appeared in the sadly short-lived Green Lantern the Animated Series as the first major antagonist. As far as backstory, the loss of his world remains the same between comics Atrocitus and cartoon Atrocitus.

However, the thing that distinguishes them is that cartoon, Atrocitus was perfectly willing to destroy whole planets that resisted him. He was willing to cause the kind of damage that made him form the Red Lanterns in the first place. He was willing to become that kind of monster. Comics Atrocitus, by contrast, will not do that. He was willing to call a truce with his enemies in order to prevent a universe-wide massacre.

Does that make the cartoon version a bad character? No. It just makes him more flawed and far more over the edge than the original.

Let's go back to Danzo. He admits, I think at the point of his death, that he loved Hiruzen as one would a brother. This is in the manga. However, in the anime, specifically, Yamato's anime original backstory, he attempts to have Hiruzen assassinated in order to take the Hokage position. In fact, Boruto throws in a second attempt. These actions make any admission of brotherly love later on rather contradictory...unless the brothers you're talking about are Cain and Abel.

Like in how there's a distinct difference in the adaptation of Atrocitus, I think it's important to define two different versions of Danzo, the one in the manga  who has at least one line he won't visibly cross, and the one in the anime who will totally cross that line to achieve his goals. If you're writing fanfic, which one you want to use is up to you. Personally, I think I'd prefer the anime version.

Manga Danzo will not harm Hiruzen. Other Hokage? Sure. Hiruzen? No.

But don't think the manga vs. anime thing stops there. As I was drafting this, I came to realize just how important the distinction between the two is when it comes to the subject of Danzo and Root. These differences will be highlighted throughout the discussion.

Root: The Organization That Has No Reason To Exist

The idea behind Root, or the Foundation, if you prefer, is that it's a subdivision of the regular ANBU under the direct command of Danzo. Hiruzen let Danzo take on the village's darkness, or so canon says, allowed him to form Root to take on the sort of dark things that Hiruzen himself didn't want to handle, the sort of things too nasty for even regular ANBU. It makes sense, doesn't it?

...Doesn't it?

As Kakashi once said, see underneath the underneath. So, I challenge you to not take that train of thought at face value, and instead look a little deeper, below the surface. I ask you this question: What exactly was Root supposed to do? If you say "whatever Danzo wanted," then you're wrong, because that's not what I mean. What I'm asking is what was Root intended to do? What did Hiruzen expect them to do? What did he expect Danzo to handle exactly?

Some of Root's known missions include infiltrating the various hidden villages, but that can't be it, because infiltration and spying aren't that dark, and if you think that's too much, you're in the wrong line of work. Assassination, then? No, that can't be it, because assassination is literally the A in ANBU's name, Ansatsu.

There was the time Danzo assisted Orochimaru in experiments with reviving Wood Style, but that was illegal under Hiruzen's orders, so that doesn't count. So, I repeat, what was Root supposed to do? Steal the recipe for Sand Dumplings from the Land of Wind? Graffiti the walls of Kirigakure and proclaim the Third Mizukage has no eyes? Act as extras in haunted house attractions?

Root was supposed to be a new element to the story, a vehicle for an antagonist. Metaphorically, it should be a delicate mechanism constructed from real world logic and narrative/internal logic, moving in time with the story's larger clockwork. Root appears that way at first, but if you look deeper, you will find the smoothly operating machinery is just a bunch of broken gears and springs.

Why hand Danzo what amounts to his own private army? If you need people to do really nasty missions, then why not form a squad for when those things come up, rather than an entire division? How often do these situations come up, these situations that are too much for the black ops assassins?

Root makes no sense because it has no in-universe reason to exist. It had no real reason to form in the first place because functionally-speaking, there's no real, visible difference between what the regular ANBU do and what Root does, so why even create them? 

Root: The Massive Plot Hole That Destroys ALL of Shippuden (And the Original Naruto, Too)

The only reason Root exists is so Danzo can use them for his underhanded deeds, and that's not good enough. Without a solid in-universe reason for this organization to exist, to have been officially formed, the whole concept becomes a plot hole. In the process of writing this world building series, I've found more than one continuity error or plot hole, and some of them, you could argue, do not effect the plot that strongly.

This, however, does because (pardon the pun) Root is part of the foundation of Shippuden's story. In fact, it's also a central support of Part 1's story as well.

Imagine that a story is a stained glass window. An intricate work of glass in a variety of colors, displaying people, places, creatures, and events from the depth of the imagination, glowing with the light from either the sun or moon. Now imagine such a window for all of Shippuden. Ninjas stand together on this pane, a giant tree looms overhead. Monsters roar in the distance.

Beautiful image, isn't it?

But a plot hole? A plot hole is a crack that, once discovered, will begin to spread. Root's lack of reason to exist within the story is our crack, and it's primary consequence would be that Root simply fails to exist at all. How can it, when it has no solid reason to? In fact, Danzo himself would also fail to exist, since they're a package deal. 

It doesn't stop there, either. For some of you, the consequences of Root and Danzo disappearing from the story may be obvious, but to summarize, here's the damage we're looking at. Also note that a few of them require a little more in-depth commentary, so there will be some plot hole discussion sections after this.

1. Sai no longer exists. (Manga and anime)
2. Yamato no longer exists. (Anime. See Plot Hole Discussion #1)
3. If you like Boruto, Inojin and Sumire no longer exist. (Manga and anime)
4. Kabuto's entire backstory no longer exists. (Manga and anime)
5. Fu Yamanaka and Torune Aburame no longer exist (Manga and anime)
6. The Uchiha Massacre does not happen. (Anime and manga. See Plot Hole Discussion #2)
7. Minato and Kushina live because the Uchiha were there to help subdue Kurama (See Plot Hole Discussion #2)
8. Shisui doesn't die. (Manga and anime)
9. Nagato does not become Pain. The new Akatsuki never form. (Anime and maybe manga. See Plot Hole Discussion #3 for this and all remaining points)
10. Hanzo of the Salamander does not die.
11. The Pain Assault arc does not happen.
12. Jiraiya does not die.
13. The Fourth Mizukage does not die. Mei Terumi does not become the Fifth Mizukage.
14. The various other jinchuriki Fu and Yugito do not die.
15. Madara's plan never comes to fruition.
16. Kaguya never gets free.

I know several of those don't sound like bad things, like the various characters living, but the point is that if you wanted the story to go in any of those directions at all, you're out of luck, because they can't. Root isn't just some isolated story element. It was used to support basically all of Shippuden's major events. Without it, the crack in our stained glass window becomes unbearable, and the window shatters, reducing our beautiful image, all of Shippuden, to a sad heap of disconnected plot shards and characters laying below an empty frame.

Anime vs. Manga Plot Hole Discussion #1: Yamato

In doing research for this analysis, I have realized that Yamato's entire connection to Root and Danzo is anime-only. It's not just his backstory, but his whole connection. Look at the Narutopedia article on him for yourself. Of the fifty references used there currently, only thirty-one are for the manga and/or databooks, things worked on directly by the author.

Those references only establish his abilities, his personality, his appearance, his status as an experiment of Orochimaru, and his time in ANBU under Kakashi. The Third Databook does say that his nickname is Tenzo of the Wood Release, which is interesting, since Tenzo was associated with the Iburi Clan in the anime, and yet this databook came out (in Japan) six years before the relevant anime episodes came out (also in Japan).

The Fourth Databook calls him "Kinoe," which was his Root codename, but this book came out several months after the relevant episodes (in Japan), which could mean that Kishimoto was pirating details from the anime. Regardless, if you're going by manga/databook continuity, then Yamato is just an Orochimaru experiment that got into ANBU under Kakashi, and that's it.

Anime vs. Manga Plot Hole Discussion #2: The Nine Tails Attack/Uchiha Massacre Plot Hole

If Danzo doesn't exist, then he can't manipulate Itachi into committing the massacre in both the manga and anime. Right off the bat this destroys a good chunk of Shippuden's story, but the damage is actually far worse than that, causing not only the story's second act to shatter to pieces, but also the first.

Some of you may have read or remember how Danzo stopped the Uchiha from helping contain the Nine Tails during the attack. This plus all the subsequent mistreatment pushed them towards wanting a coup. However, that plot point is not in the manga or databooks. When Obito tells Sasuke the truth starting in chapter 400, he simply says that the village was suspicious of the Uchiha in the wake of the attack, causing them to be moved, and this, combined with more undefined mistreatment, made them want a coup.

This plot point came from the anime, established in Shippuden episode 358, part of the Kakashi ANBU arc mentioned in the previous entry in this world building series. It was then reused in the novel Itachi Shinden: Book of Bright Light, (English Naruto: Itachi's Story. Vol 1: Daylight), and was mentioned again in Shippuden episode 452 in the "Itachi Shinden: Book of Light and Darkness" arc, which was just an adaptation of the two Itachi novels.

You could say that this is the anime attempting to use Danzo to redirect the blame off other characters, and was clearly a terrible idea, but in actuality, this plot point is a good one. Whether the writers realized it or not, this little inclusion actually plugs a very serious plot hole in the story. Yes, another one.

It was in the Shippuden part of the story, chapter 309 to be precise, that it was established that the Sharingan could be used to control tailed beasts. That's the regular Sharingan, not the Mangekyo. Once this was made true, it destroyed the whole story up to that point.

If the Nine Tails is running loose, and you have an entire clan full of people that could help corral it, then why didn't any of them help? In the very beginning of this series, we see ninja throwing kunai at it. Sending those guys in as opposed to the literal tailed beast wranglers is like calling the police to the scene of a house fire instead of the fire department. It makes even less sense that none of the Uchiha would try to help defend their home.

If you want the Sharingan to have that ability, then clearly, something has to stop the Uchiha from helping, and Danzo honestly makes sense. He could have decided to use the situation to help him deal with a clan he considered a threat, intending to blame them in the first place.

Or perhaps blaming the Uchiha was just a convenient secondary benefit, and Danzo just wanted Minato to die so that he could have another shot to be Hokage. Danzo did the same sort of thing to Tsunade when Pain attacked (in both the manga and anime), so this is actually perfectly in character for him.

It is unfortunate, then, that the plug for this serious plot hole was another serious plot hole, compounding them both. Remove Danzo and Root from the plot and you reopen this plot hole, destroying the entire Naruto series right from the very beginning. 

Anime vs. Manga Plot Hole Discussion #3: Nagato

This one is actually a bit tricky. Nagato became Pain at that meeting with Hanzo, the one where Yakihiko died. As far as the manga and Danzo are concerned, Danzo and his Root agents were there. He'd teamed up with Hanzo so he could get aid in becoming Hokage, while the other wanted help securing his position. In the anime, Danzo is more involved, manipulating Hanzo to turn on the Akatsuki.

Whether or not the presence of Danzo and Root was enough to capture Konan, murder all the other Akatsuki, trigger Nagato into becoming Pain and setting off the rest of the plot, I can't really say. As far as the manga is concerned, I'd say its called into question, and leaves that version of the plot a whole lot weaker than it's supposed to be. As far as the anime is concerned, the entire plot of Shippuden is ruined beyond repair. 

The Tangled, Vague Concept of Root

To be fair, the very idea of Root seems to have been confused and weak to start. Root is mentioned in the manga in chapter 284, when Tsunade calls it a former "training" division of ANBU and says that it was disbanded. She does not say why it was disbanded. Apparently parts of canon (full canon, aka the manga and databooks) suggest there was an "incident," but it is the anime and novels which directly connect its disbandment to the Uchiha Massacre.

And to also be fair, the idea that "Root was formed to handle the stuff too dark for regular ANBU" may only have come from statements made by the anime. I can't be certain whether it's canon, optional canon, or fanon. However, there doesn't really seem to be a given reason that Root was created in the first place, other than to serve Danzo, that is.

Follow the idea with me. Hiruzen becomes Third Hokage. At some point in his first term (this makes the most sense both narratively and time-wise), he decides there are dark things involved in running the village he doesn't want to deal with, so he puts Danzo in charge of that stuff. Not exactly the best motivation, but delegating can be good in general. The point is that Danzo creates a sub-division of ANBU called Root which he is given direct command over. 

That's a major point: Root is referred to as a sub-division of ANBU, and as a "training" division. Let us say that Danzo decided to form Root for his own purposes, for his own goals, and did not inform Hiruzen about it. If so, Root, being invisible to the Hokage, cannot be called a sub-division of ANBU.

The fact that it was called as such means that at one point in time, it was an official organization known to the Hokage. Whether or not it was known to regular ANBU is a different question, though I would think it would make more sense for it not to be.

Calling it a training division invites more questions and confusion, if that title was meant to be taken as accurate. It could have just been called that on paper. But imagine for a second that it was created to officially be a training division, that this is what Hiruzen was told it was. If so, then wouldn't that mean there would be no "Root agents"?

If it was just for training, then Danzo would not have ANBU of his own, technically, because they'd all just be regular ANBU. So, was "training division" was just a cover? If it's a cover, that brings us right back to the question of what Root was supposed to do, and the void where the answer should be.

The novel Itachi: Book of Bright Light says that Root was something like a "secret police force keeping public order from underground," and that as far as the Konoha Military Police were concerned, it and Root were "two sides of the same coin."

However, this cannot be taken for their official function, as this statement is made in a scene that's in Danzo's POV, so we are hearing his own knowledge and opinions. The same novel also calls Root a training division, but again, if it is meant as its actual function on paper, then there would be no true "Root agents," and any distinction by the characters would make no sense.

Root's Rules Are Never Followed (Unless It's Convenient)

One of the things about Root is that all the members (save Danzo, naturally) get a curse seal on their tongue that prevents them from saying anything incriminating about Root and/or Danzo. For a man doing shady things, it's a smart move.

But in the previous part of this world building series, I pointed out how Yamato's anime backstory has him clearly violating this rule in a way that should have divorced Danzo's head from his neck...or at least moved him to prison. Neither of those things happen thanks to the Idiot Plot nature of the whole thing, but the violation is there.

And then there's Shippuden episode 44. At the very end, after finding out that Sai left with Orochimaru, Yamato speculates, out loud, that "Danzo may be plotting the destruction of the Leaf Village." I am not sure if canon ever says flat out that the curse seal prevents members from giving away incriminating information about Danzo and Root, but logically, that's the way it should work. If Yamato is a former Root member, he should not be able to say something like that, even if it's speculation. Think it, sure. Say it, no.

This, of course, can be explained by the fact that all of Yamato's Root connections weren't established until several hundred episodes later, but where anime continuity is concerned, this is a problem.

In episode 48, Naruto, Yamato, and Sakura find Sai, who has just gotten a room in Orochimaru's hideout. They accuse Sai of being a go-between for Danzo and Orochimaru, and that the two are planning something big. Now, to be fair, Sai stays quiet during these accusations, which could be a sign of a working curse seal.

But then he says (this is the dub translation, but that translation is faithful), "You are correct. The plan was to crush the Hidden Leaf Village. My true assignment was to form an alliance with Orochimaru, and to orchestrate a conspiracy with him, so that together, we could destroy the village. The other half of my mission was to gather intel on Orochimaru, in short, to report his activities back to Lord Danzo."

Yamato tells Sai to own up to everything he's hiding, and Sakura says that gaining Orochimaru's trust to defeat him later sounds like a suicide mission. Sai says "If the Leaf Village did fall, we fully expected Orochimaru would try to betray us. But this way, we always have the advantage over him."

Yup, that's right, Sai blabs the whole thing. He even talks about how his name is fake and how he's just a tool for Danzo. By episode 51, we learn that Sai's real mission was to assassinate Sasuke, and he says that to Sakura and the others.

Now, one could say that Sai's statement about being a go-between for Danzo and Orochimaru to destroy the Hidden Leaf was a lie because Kabuto was in the area. However, I'd still argue that Sai should not even be able to say something like that, even as a lie, because said lie is a confession of Danzo committing high treason. It also makes no sense that Sai was still able to spit out the fact that he was sent to kill Sasuke.

One could argue that perhaps the reason for Sai's easy blabbing is because the actual concept of the curse seal wasn't introduced until chapter 452 (the manga's Pain's Assault arc), and Shippuden episode 197 (the anime's Five Kage Summit arc). And you might be right. The idea might not have occurred to Kishimoto until that point. But this does not fix the problem. Even without a curse seal, you'd think Sai would have been trained not to say things like that so easily, and Danzo is still in serious hot water.

Anybody reading the chapter/watching the episodes in real time would still see the plot hole, and if the seal is indeed some kind of retcon, it breaks that part of the story and only exacerbates said plot hole.

What's Known About Root Post-Disbandment

Here's even more confusion. In chapter 284, Tsunade is forced by the council (Koharu and Homura) to have the third member of Team Seven picked for her, and that pick is made by Danzo, who apparently has only shown his face at that point. That is already a little weird to me. Danzo may not be on the council, but he hasn't appeared in front of Tsunade in years? Anyway, the appearance of Danzo makes Tsunade instantly worry that the third member will be a Root agent.

A few interesting factoids come up in this conversation, and Tsunade's subsequent conversation with Yamato. One is that Sai is referred to as a member of Root, and not a former member. If Root was officially disbanded, then why would he not be considered a former member? His status should be past tense, not present.

Furthermore, Sai being a known Root agent is...wobbly. As mentioned before, other sources ended up pinning the disbandment of Root with the Uchiha Massacre, which happened eight years after Naruto was born. If you look at the timeline created by Seelentau, you will see that Sai becoming a genin would have been, at minimum, several months after the massacre.

The fact that Sai is still considered a member of Root could suggest that the incident that lead to Root's official disbandment was later than the Uchiha Massacre. But if it wasn't, if we instead pin the disbandment to the massacre, or even earlier than that, calling Sai a Root agent becomes strange. Does this mean Hiruzen and/or Tsunade think Root is still active? That would be cause to arrest or investigate Danzo because, you know, Root was supposed to be disbanded.

In episode 35 (A canon episode, and this scene is also in the manga), Tsunade tells Sakura that Danzo is "Sai's superior." Again, present tense, not past. This connects Sai to Root, and could imply that Root is still officially active, which blatantly contradicts statements from the previous episode that Root was disbanded.

If saying it like that means Tsunade thinks Root is unofficially still active, then why hasn't she done anything about a serious threat? Say what you will about Hiruzen hesitating, but Tsunade is not like that. She will only hesitate when making a plan, but for her, a will to act is not a problem.

Other Root Nonsense, and Danzo's True Power, aka "Danzo of the Plot Armor"

When you look at all the things Danzo has been involved in, it appears, at least to me, that Danzo's true power isn't his multiple Sharingan, or his MacGuffin Hashirama Cells, but rather, it's a suit of Plot Armor. Plot Armor is a trope that normally applies to the protagonist of a story, referring to when they survive something that really should have killed them, but it can also apply to other characters as well.

To illustrate, let's go through the various parts of canon where Root has proven to be more plot device than a fully-functioning plot point.

The Tenchi Bridge Arc (Anime and Manga)

I already mentioned Sai's confessions in this arc earlier, about his meeting with Orochimaru, his mission to kill Sasuke, etc. But there was more to it than that. In the story, Sai proves his value, and Danzo's sincerity for an alliance with Orochimaru by presenting the Sannin with a manila envelope, the kind you tie with a string.

Inside this envelope was a stack of papers containing information on ANBU working directly under the Hokage, complete with faces. I would think all ANBU technically work under the Hokage, but whatever. The point is that ANBU identities are supposed to be secret, so this is a big deal.

When Orochimaru, Sai, and Kabuto return to their hideout, Orochimaru gives Kabuto the information, telling him to make a bingo book out of the data. Kabuto is also asked to show Sai to a room. Kabuto does, and ends up leaving the envelope on the bed accidentally. It is seen sitting there in both the manga and the anime.

Kabuto leaves the room, before later realizing he left the envelope, and begins heading back for it. At the same time, Team Kakashi has caught up with Sai and begins interrogating him, getting the information mentioned earlier. Kabuto's return provides tension to the scene. When Kabuto returns to the room, everyone, Sai included, is gone.

As far as the envelope, we see it on the bed when the team interrogates Sai, but when Kabuto returns, well, it's not that the envelope is gone, but rather that it's just not in frame. This is true of the manga and anime version. We never see the team interact with the thing, and as far as the story is concerned, the envelope has pretty much vanished into the aether.

In the manga, at the very end of the arc, when Team Kakashi is giving their report, we don't see the team say a word about what happened. We only cut to Tsunade saying "I see..." and then the discussion about Sai staying on the team. That's it. No mention is made of Sai's real mission, or the envelope, whether it was recovered, nothing. It's not like the envelope would have been hard to spot for the team, so they could have picked it up. Like I said, the thing just seems to vanish, like Chuck Cunningham Syndrome, but applied to an object.

This is a serious problem where Danzo is concerned. Consider the facts:

1. Sai's cover story basically testifies to an act of treason by Danzo.
2. Sai openly admits that his real mission was to kill Sasuke. While Sasuke is a missing-nin, Tsunade's orders in regard to him were to bring him back alive, meaning Danzo ordered a mission that went explicitly against the Hokage. This also lands him in trouble. Not as bad as the previous point, but still serious trouble. Danzo is not even on the council anymore. Earlier canon data says he's "out of power."
3. The envelope contained classified data on the identities and statistics on various ANBU. If this data is real, and it may very well have been, the manga neither confirms nor denies this, that means that even if the "I'm plotting to destroy Konoha" thing was a lie, Danzo used real, classified data as bait without permission. Again, that would automatically land him in serious trouble.
4. Team Kakashi also discovers Sai's Root bingo book which indicates that Sai took out a jonin from the Hidden Mist who simply expressed a bad opinion of Konoha. Really hope it was for better reasons than just "your village smells of elderberries," but the point is, this is evidence that Danzo ordered a hit on an international target without Hokage approval. Again, he lands in trouble.

In the anime, the situation is rendered even worse for Danzo. The ANBU data is confirmed to be accurate, both by Orochimaru (Yamato's picture is seen in the set), and by Tsunade.

Yes, at the end of the anime version, there's an extra scene where Yamato does the smart thing and tells Tsunade all about Sai's real mission. Furthermore, he actually retrieved the envelope. Tsunade takes one look at it, realizes it's legitimate, and orders Shizune to increase security on the secret archive, wondering how Danzo got his hands on this.

Danzo should have gotten in serious trouble. Envelope or no, all it would have taken was the team just saying something about Sai's mission, or Sai just saying something. But...he didn't. None of them did. Not in the manga. Not a single visible word. If they said something off panel, it's never indicated, nor are there any apparent consequences in the plot. Pain's Assault is right around the corner, but before that is Asuma's death, so it's not like Tsunade couldn't have done something in response. But there's nothing.

Tsunade is not going to spare Danzo for friendship reasons like Hiruzen might (or might not, as indicated firmly by the anime). The Hokage is the Hokage, and even if Danzo is still on the council, does it seem logical to you that he could just countermand the Hokage's direct orders like that?

The council is supposed to be made of advisors, but the Hokage is supposed to be the ultimate decider. Then again, I also remember a moment in chapter 400 that said with regards to relocating the Uchiha, Hiruzen was "overruled." It was a fan translation to be fair, but if it's accurate, then the series is confused as to who can do what.

The Yamato Situation (Anime Only)

I will not repeat the very long episode by episode dissection I did in the previous part of this world building series. Instead, I'll give you a summary. I am speaking of the part of the Kakashi ANBU arc, which is anime original, and which establishes Yamato as a member of Root. In this collection of episodes:

1. Danzo was caught attempting to assassinate the Hokage, but was forgiven just this once under threat of execution. 
2. Yamato confessed to being sent to help Orochimaru escape capture, but Kakashi says nothing about it.
3. Kakashi testified that Yamato was sent to kill him and steal his Sharingan.

The Twelve Guardian Ninja Arc (Anime Only)

This original story provides space between the Tenchi Bridge arc and Pain's Assault/Asuma's death. To the anime's credit, the issue of Danzo is followed up on, showing continuity between the anime-only elements. Tsunade, swamped by problems on multiple fronts, decides to first tackle the problem closest to home, and sends ANBU to watch Danzo, something he's well aware of.

Things come to a head in episode 64, when Danzo is caught by a team of ANBU while going out to talk to a ninja from the Hidden Rain. There have been attacks on border villages lately, and the Hidden Rain has been suspected. The ANBU that capture Danzo remark how it was Danzo who taught them that when facing a superior opponent, make up for quality with quantity. This again ties back to Root being called a "training division," and that Danzo trained all ANBU, but again calls into question of why there are Root agents in the first place.

In any event, Danzo is actually hauled off to T&I along with the ninja, where Tsunade is waiting. Yamato recognizes the Rain ninja as Tatsuji. He was in the Leaf ANBU, but went missing when Yamato was still part of ANBU. Ibiki is brought in to make Tatsuji talk when suddenly Koharu and Homura, the most useless elders in the world, barge in protesting Danzo's treatment.

They knew about Tatsuji, and say that he was sent by Danzo to infiltrate and spy on the Hidden Rain. In fact, Tatsuji was also passing information to them as well (something that surprises even Danzo, from the looks of it). Danzo then takes an opportunity to berate Tsunade for being incompetent for still thinking the Hidden Rain might be responsible for the attacks, how her moderate policies are weak, etc, etc. Before the interrogation can go any further, Sora, the character unique to this arc, is caught eavesdropping and everything quickly turns to chaos.

I do appreciate that the anime tried to follow up on the envelope plot point from the previous arc, but it still fizzles out very quickly. For one, it's shocking that Danzo's informant was also passing information to the other elders. Was this guy not a Root agent? Does Danzo not have control over his own agents? Danzo legitimately looked surprised, so what was his actual plan to lose the ANBU tail and divert suspicion? He had to have one.

Second of all, there's Tatsuji. This guy was in ANBU and went missing. He was also in the squad when Yamato was around, but given the timing, Tatsuji going MIA could have been as recent as weeks or maybe a month. Even still, are you telling me that Danzo and/or the council were okay with letting an ANBU just up and go missing without informing the Hokage? Is it okay for any of the elders to just assign a mission like that to an ANBU without telling the Hokage and getting their approval? In a way that wouldn't automatically get you in trouble?

Ever heard the phrase "Circle of Trust"? As far as the Konoha Council is concerned, it's one giant Circle of Disrespect. None of the elders seem to have any respect for the authority of the Hokage at all. Perhaps it's a matter of personal feelings, though I have no idea why. Tsunade certainly doesn't like any of them, but it's not like they've ever been anything but a problem.

I could suggest that perhaps the council was so used to Hiruzen delegating and being a pushover, and their ideas getting the green light, that coming into contact with a strong-willed leader like Tsunade is something Koharu and Homura just aren't used to. But then, it would make more sense for this problem to be present in Part 1, and not after Tsunade has been Hokage two to three years. You'd think those two would have learned who was in charge.

Apologies for the digression. In any event, the thing with Danzo is pretty much over at that point, and sadly, the envelope vanishes once again into the aether, even though it would be solid evidence that should earn Danzo a long term stay in a jail cell.

The Five Kage Summit (Manga and Anime)

When Danzo is at the Five Kage Summit, he uses Kotoamatsukami, Shisui's powerful brainwashing jutsu, to try and ensure Mifune, the leader of the Land of Iron, chooses him to lead the united shinobi forces.

Unfortunately for him, Ao of the Hidden Mist has the Byakugan, and not only recognizes something is going on, but also recognizes both the chakra and the jutsu as belonging to Shisui Uchiha, and interrupts the meeting. Danzo is forced to break the jutsu, and his act is discovered in front of an international crowd.

The other Kage are naturally very angry, although Danzo himself is strangely calm and unapologetic for being discovered. He even comments how he can't even use the technique that many times a day. You know, like a casual excuse. Perhaps he's merely grown bolder and more deluded. It was awfully risky doing that in front of an international crowd, and since he got caught, I wonder if he shouldn’t be more...worried. After all, he hasn't actually secured the Hokage position yet. 

The Hidden Mist ninja (Ao and Chojiro) are ordered to guard him and make sure he doesn't move, and before any other consequences can happen, Sasuke's break in is noticed, everything hits the fan, and ultimately, Sasuke kills Danzo.

Fu Yamanaka and Torune Aburame (Anime Only)

In Part 3 of this world building series, I briefly discussed Fu Yamanaka and Torune Aburame and how their backstories didn't really make much sense based on timing alone. I fear I may repeat myself when I get to this on my timeline, but let's talk about them again.

Torune’s recruitment backstory is an anime-exclusive thing, occurring in Shippuden 317. People on Narutopedia’s Discord server told me that Danzo tended to recruit kids into Root when they were 10-12. In any case, shortly after being recuited, Torune met Fu, and Fu looked like he was around 10-12. 

Now, Fu was recruited into Root first, so let's do some math. For those who have not looked at the first part of this series, know that I'm using my own year measurement system. The numbers are all accurate to canon data, I just converted them to positive numbers to make them easier to work with. Just subtract 50 to make them relative to Naruto's birth.

Fu Yamanaka was born in 48 KY. If he was 10-12 when he was recruited, then that would mean it happened in 58-60 KY. However, the Uchiha Massacre happened in 58 KY. According to Seelentau, it happened at the latest July 22nd. Once Root is disbanded, Root will have a hard time getting new members, so Fu's willing recruitment is in question.

As far as Torune, it's even worse. Follow along with me. He was born in 47 KY, so he's a year older than Fu. But with Torune, it's not so much his age that's the issue so much as the age of all those around him.

Danzo arrived one day at the Aburame compound, wanting to recruit Shino into Root. All the clans with hidden jutsu such as the Yamanaka and the Uchiha had sent candidates. Shibi, Shino's father, asks if this has been approved by the Hokage, and Danzo replies that when it comes to Root, he has sole jurisdiction, and this is not so much a request as an order. Torune ends up volunteering instead, though for him it's very casual rather than "I will sacrifice myself for you."

Back to the age thing. Shino looks like he's under ten years old in this flashback. That means Torune was recruited before 60 KY. This puts Torune's recruitment in the same nebulous, or perhaps the better word is tenuous, territory as Fu. But it actually gets worse. In the episode, Torune asks how Shino is adjusting to the academy, as if he'd just started.

Again, Shino, and even Kiba and Naruto, all look under ten years old, but they also don't look like they're six. Why do I say six? According to canon data, Sasuke started the academy when he was five years old. Seelentau's timeline placed this event in April of his sixth year of life, 56 KY.

There is no reason to think that Shino would not have started school at the same time, or even a year earlier, since his birthday is in January. Five is a rather typical age to start real world school, and I could cite the fact that Kakashi, Obito, and Rin all started the academy at age five, if not others in their class like Asuma, Kurenai, etc. So, Torune's discussion with Shino is very strange.

But, if you can believe it, the situation gets weirder still. Iruka is also shown in this flashback, already a teacher and on friendly terms with Naruto.

The anime actually tackled the subject of Iruka's teaching career in the first few episodes of "Past Arc: The Locus of Konoha," the anime original arc set after Pain's Assault. Specifically, I'm referring to episode 176. In that episode, Iruka begins at the academy as Naruto's teacher, and it's established that Sasuke has already lost his clan.

This would place the episode at minimum in 58 KY, or more probably 59 KY, if Iruka had started at the beginning of a new school year. So, if the anime were following its own continuity, Iruka being in this flashback means it happened in 58 KY, minimum, after the Uchiha Massacre. The episode's factoids are all over the place.

If Fu was recruited before Torune, and if he looks 10-12, that means Torune can't have been recruited before the Uchiha Massacre, which also lines up with the presence of Iruka, and that would make Danzo's actions frankly bizarre.

Think about it for a minute. Danzo is attempting to recruit Shino in a face to face meeting with the head of a major Konoha clan, mentioning Root by name, and saying he has the power to do this by the Hokage, probably the year after Root was officially disbanded. This tactic depends entirely on silence, and no steps are taken to ensure that silence.

All Shibi has to do is say something. It doesn't even have to be an angry demand. He'd merely have to ask a question or make a comment to Hiruzen. He could just say five simple words. "Danzo recruited Torune into Root." He could ask about this whole "Root" thing. Hiruzen would stop, blink, slowly turn his head and say "...Danzo did what?" The next thing you know, ANBU are kicking in Danzo's door and dragging him into a very not cozy jail cell, and Torune and Fu are sent home.

This is why his real power is Plot Armor. Danzo, most especially in the anime, has been busted multiple times doing clearly illegal things. Characters have had opportunities to do something about him if they only say something, whether it's Team Kakashi, Kakashi himself, or Shibi Aburame. Just opening their mouths to speak would do it. They just don't. It's like some kind of reverse logic where everyone other than the Root agents has that curse seal on their tongues.

Of course, they don't have that seal, so what's the problem? The best answer I can give is because Danzo is needed further in the plot. He needs to be killed by Sasuke in a big dramatic scene to fulfill the vengeance quest or whatever. Or it's that these actions, like with Yamato, are in the past and Danzo is needed in the present.

He is immune from all consequences until the plot requires him to die, less involved in the series' present story as much as woven into the backstory, and it's all done in so clumsy a manner that a suit of Plot Armor is the only way it could ever work, and that harms the series more than it ever helps.

Leaking Naruto's Secret (Novels)

One last thing I'd like to comment on. I know it doesn't entirely fit into this section, but I wasn't sure where else to put it. In the second Itachi novel, and only in that novel, it is established that Danzo himself is the reason Naruto's jinchuriki status got leaked to the villagers. This was done because Danzo thought the village was stronger when it had someone or something to hate, that because the villagers blamed Naruto, they maintained emotional balance or something like that. Honestly, the entire conversation was a bit...I want to say pretentious.

The decision itself is rooted in personal beliefs on human nature, but there's also a certain lack of logic, there. It antagonizes the child with the powerful monster inside of him, a jinchuriki, who villages often view as living weapons of mass destruction. Antagonizing a jinchuriki like that is not likely to end well (see Gaara). For this reason, Danzo's decision appears weird and nonsensical.

Obviously, the information leaked somehow, and if we were to trace that leak back to a deliberate decision on Danzo's part, there is one alternative motivation I could suggest. Perhaps he did so with the intent of maneuvering Naruto into a more vulnerable position. Without support from the village, Naruto would be easier to manipulate by Danzo, so that Danzo could have control over him. Obviously, this did not work out, and only a possibility, but that could be a motivation.

Danzo Should be INCAPABLE Of That Level of Incompetence

There are many words one can use to describe a character like Danzo Shimura. Most of them are obscenities. He is most definitely not a good man. I don't think he even qualifies as a nice man. But I think it's safe to say that he isn't, or rather, shouldn't, be a stupid man.  

After Pain's Assault, when he was the Sixth Hokage Candidate, Sai asked him what he was going to do about Naruto. Danzo said that he wouldn't do anything yet, as Naruto was the village's hero right now, and he still needed to secure the vote of the jonin to ensure his becoming Hokage. That is the sign of a man with brains.

A pity several other instances make him appear very stupid.

In concept, Danzo is supposed to be a shadowy manipulator, right? The man that works in the shadows? That's his entire thing. If you go with the idea that Root was an official organization that was later officially disbanded, then the moment it is should be Danzo's time to...not shine. It's the moment where as far as being a shadowy manipulator goes, the rubber meets the road, where Danzo should prove to us all that he truly is good at it, that he can be the very best manipulator, like no one ever was!

If you want Danzo to function properly, to be the Chessmaster he's supposed to be, he has to be smarter than this. He can't recruit Torune the way he did after Root is disbanded. I have seen a fanfic or two talking about children kidnapped from their beds, and that makes much more sense. If anything, that's what I would suggest with regards to those Fu and Torune.

If you want him to stay in the story, you can't just power through him getting busted or deck him out in Plot Armor and have him avoid consequences "just because." You cannot have people stay silent against all logical thought. As the expression goes, work smarter, not harder. Use your brain, not your brawn or Plot Armor. Using Plot Armor repeatedly makes all of your characters look like idiots, and does more harm to your story than good.

And no, you can't use Izanagi to get out of it, either. That's a cheap plot device to begin with that was created as an easy escape when you write yourself into a corner.

This, of course, does not mean that Danzo cannot make mistakes, or that he can't nearly get caught, or even that the incident where Hiruzen busted him post-assassination attempt can't happen. But if he gets busted, he needs to be especially cautious in his activities. Root is supposed to have been disbanded in the manga, right? Being disbanded, and Danzo "removed from power" implies that Danzo did get caught at something. But he can't keep getting caught.

Hiruzen, as I expressed in the previous part of this world building series, is the sort of person that will act if the village is threatened. He is simply unwilling to act at times, not unable, and there's a big difference between the two. A smart man would know that difference and know not to press his luck too often, though hubris and obsession may weaken that intelligence and allow him to suffer for it. 

A character like Danzo should not be on the same intellectual level as the sort of person who commits a crime and then taunts the police about it on social media while also uploading video evidence of said crime to said social media. If he is, you have failed monumentally, and need to retrace your steps. 

A Loose Historical Comparison: Danzo vs. Jonathan Wild

Forgive me this little digression, but it's a weird comparison that's been rolling around in my brain. Jonathan Wild was a real person who lived from 1682 (or 1683) to 1725. He was known at one point as the Thief-Taker General of London, and in a very loose sense, his story can be used as an illustration of the difference between the current messy Danzo vs. a much more functional Danzo.

In the 18th Century, Jonathan Wild was the city's number one law enforcement guy. He was not the chief of police, mind you. The police did not exist. Thievery was on the rise in this time period, and in London, Wild was the solution, a town hero, a fighter for justice!

People loved Wild. But in reality, Wild was London's biggest crime boss, and his entire operation was a giant scam.

Now, this operation was not Wild's to begin with. It started with a man named Charles Hitchin. Hitchin used his position as a front for a blackmail and extortion scheme, and even led his own gang of thieves. Jonathan Wild, already a criminal by that point, had been hired by Hitchin as a deputy. But the way Hitchin ran things was...not good. Not that it was good in the first place, but you'll see what I mean.

In the process of his extortion, blackmail, and running the city's thieves, Hitchin had a lot of face to face meetings. He charged large amounts of money, both in terms of the cut he took from his thieves, and what he charged his victims, which alienated both. He also signed blackmail letters with his own name.

Doesn't sound very bright, does he? Wild certainly thought so. In fact, the reason Wild was brought on is because Hitchin got caught in an anti-corruption investigation. He didn't serve any jail time, and was allowed to keep his job, but he had to step away from it for a few years. Hence, Wild was put in charge.

Now, here's how Wild ran the same organization. For one, he charged less, letting his thieves keep more of the loot. Two, no more blackmail letters. In fact, the usual scheme went like so:

You’re walking along the street, minding your business, when you are beaten and robbed. You go over to Wild’s office, where you describe the attack and what got stolen. In a couple days, Wild reports back that his agents have found the thieves. He then negotiates a ransom to get your stuff back, and you perform the exchange in an anonymous meeting. 

Thanks to Wild, you get your things back, and Wild only charges a very modest fee for his hard work (he wasn't government funded, after all). You walk out of his office, reunited with your valuables, thinking how heroic Wild is. What you and everyone else on the street doesn't know is that the thieves that robbed you work for Wild. He's not only pocketed your fee, but he's taken a modest cut of the ransom you paid his own thieves.

Since the only money he touched was what you paid him directly, there's no evidence he was behind the entire thing, and believe it or not, that's only scratching the surface of the tricks he incorporated to keep himself going.

Wild and Danzo have some things in common. Both are men who operated large organizations hidden from public knowledge, performing criminal actions for their own personal ends. Both were ultimately despised by the public for their crimes (Wow, was Wild hated...), and both were ultimately undone by a young upstart: Sasuke in the case of Danzo, and a man named Jack Shepherd in the case of Wild.

And yet, the Danzo we see in the manga, and more especially the anime, operates his organization much more like Hitchin than Wild. You can definitely see the Hitchen comparison in Torune's backstory. This is again what I mean by working smarter, not harder. Hitchin was too public with his efforts, too blunt, and it came back to bite him when someone smarter came along. Wild's efforts came back to bite him, too, but in a different sort of way.

Between Hitchin and Wild, the way Danzo operates Root should be like the latter, and never like the former.

How to Fix Danzo and Root

Now that we've very thoroughly established what a bizarre mess Root is, and that fixing it is rather essential to the health of the story, the big question is how? How do we fix this mess so that it can accomplish what it needs to accomplish in a smooth, logical manner?

Thankfully, canon actually gives some ideas. I can't say what I'm about to put down is the only possible solution, but it is the one that I personally prefer. Whatever you choose in your own work, simply remember to keep in mind the points that I have discussed already, those being: 

1. Danzo getting caught (Don't be stupid about this or push it. Plot Armor Danzo is awful, and so are Idiot Plots.)
2. Root agents not being able to say anything (Be consistent with that and don't pretend that others are the ones who are cursed instead just for the sake of your plot.)
3. What is known and not known, and who knows it (There's a difference between facts and rumors. Keep this in mind when getting exposition across.)
4. If Root is an official unit of the ANBU, why was it created? (Do not create a flimsy distinction between them and regular ANBU just because. That's not how that works.)
5. If Hiruzen knows anything about Root or their crimes. (How badly does this reflect on his character and why hasn't he done anything? He's hesitant, not powerless.)
6. Timing matters (If Root was officially disbanded, you should figure out when that was as soon as possible, because once that happens, the game drastically changes.)

Danzo, the Head of the ANBU

This is actually an idea from the first of the two Itachi novels. In that novel, it is remarked that the gpublic thinks Danzo is the "general manager" of the ANBU, that his position is an administrative one. I also saw a reference to Danzo as some sort of head of the ANBU in chapter 400 or so of the manga, though I will admit that was a fan translation, so it could have been wrong.

The point is this: what if Danzo was the manager of all the ANBU?

Hiruzen found certain aspects of running the village, the "darkness," to be distasteful, and passed that to Danzo. That's canon. I remember in the Kakashi ANBU arc, episode 357, Guy requests to join the ANBU, and Danzo says he lacked "darkness."

True, ANBU guard the Hokage, important buildings or individuals, or handle super high security issues, but they are still assassins, so Hiruzen wouldn't like that aspect of them at all. So, why not put Danzo in charge of all of them? This would allow Danzo to also train all of the ANBU as well.

Root, as an organization, could therefore begin its life as a specialized squad within the ANBU that Danzo assembled for the most covert, missions, the kind where if you're caught, the Hidden Leaf would have absolute deniability, rather like, say, DC Comics' Suicide Squad/Task Force X. Root could have been very secretive to start, and as far as the rest of the ANBU knew, it could have just been a rumor, with the actual Root squad members not talking.

This Root would have been used for missions that Danzo would have considered necessary, but which he didn't want to get back to Hiruzen for ethical reasons. Hiruzen may not want to know what's going on, but if Danzo does something underhanded that causes an international incident and violates some kind of law, Hiruzen will know, anyway.

Root being very different in the beginning works for canon because of Nono Yakushi. According to her backstory, which is in both the manga and the anime, she was a member of Root, but retired from it, joined regular jonin forces, was a captain in the Medical Corps, and eventually became the caretaker of an orphanage.

Think about that first thing: She retired. From Root. I think it's safe to say that the only way the Root we know in the present allows its agents to retire is with a coffin. But if Root were different in the beginning, if it were a hidden squad, it would make a bit more sense that Nono could just retire.

We could also say that Danzo began building the full organization that is Root right from the beginning, one that Hiruzen did not know about or approve, one with agents loyal to Danzo first and foremost. So instead of Danzo being told to disband "Root" and remove himself from the council, it would be "remove yourself from the council and resign your position as manager of the ANBU."

This resolves the lack of distinction between Root and ANBU, and also the bizarreness of letting Danzo more or less have his own personal army, while also keeping Danzo involved in training. It also eliminates the confusion over "who knows what" with regards to Root being active.

That is not to say Danzo couldn't still come off to people as a creepy, untrustworthy sort, or that he couldn't express militant views. But it tempers everything so he can exist as a villain without wondering how he's still around.

Danzo, the Ex-Spymaster

Here's another idea that I think works: Make Danzo the village's spymaster. We all know Jiraiya is a/the spymaster for the village, but was he always in that position? This sort of job fits a man like Danzo, and I could even cite the first Itachi novel which states that Root had a network of spies in the village that monitored everyone for Konoha's safety. Being in charge of a spy network would also allow Danzo the resources and contacts to help him build Root itself.

Root's Training Program

Root is supposed to train its agents to be absolutely loyal to Danzo and to obey his orders, and also to disregard their emotions. With regards to the former, take a look at the history of Kabuto Yakushi.

Canon says that Kabuto was in Root, and he infiltrated all the major villages. He was so good at this, in fact, that Danzo eventually decided he was "too good," and set up a trap where Nono and Kabuto would kill each other.

Danzo deciding to kill Kabuto for being too good would fit with his un-trusting nature, this is true, but at the same time, the decision is a bit illogical, and Danzo is a logical person.

Kabuto is a very talented agent. Talent like that might be hard to come by, and could take a long time to train. Plus, if Root agents are supposed to be trained to be absolutely loyal to Danzo, then wouldn't the possibility of betrayal be nullified? That's what I would think. So this suggests to me that Root's training for "absolute loyalty" came in after Kabuto. In fact, I'd even go as far to suggest that Danzo increased his efforts to train loyalty into his agents in response to Kabuto (and maybe Yamato, too).

With regards to Root agents disregarding their emotions, as well as that whole "you are paired up with someone that you eventually have to kill" thing that Sai went through, it's worth noting that when Team Kakashi confronted Sai in Orochimaru's hideout, Yamato makes a remark about it, guessing Sai went through training to suppress his emotions.

More than that, Yamato says he's seen the same thing in the Village of the Bloody Mist, aka the Hidden Mist Village under the rule of the Fourth Mizukage. This suggests to us that what Sai went through was also not the norm in Root from the beginning, and was instead adopted around the time of the Blood Mist Village. It's possible that's where Danzo got the idea.

Where Does Root Get Its Money?

Even if Root agents don't get paid like regular ninja, and why would they, if they're just tools for Danzo, Root would have financial needs. There are weapon costs, equipment costs, construction costs for Root facilities, repair costs, medical supplies, food, money that may be required for travel or particular missions (bribery, for example), the list goes on. All of these things could add up to something significant, so, where does Root get it all?

Even if the Shimura clan were very prominent, do you think Danzo would be able to fund the entire organization from his own pocket? It could depend on the size of Root, but even if Root is small, I don't think that's super likely. Maybe not impossible, but not likely.

If Danzo was in charge of the ANBU, he could have embezzled funds from the ANBU budget to support Root. This could be true whether Root was officially on the books or not. Once Danzo is forced to resign from managing the ANBU, or if Root is officially disbanded, Danzo would lose access to that source of funding. When that happens, what does he do? 

One viable solution is for Root to operate something like a criminal organization, and utilize front businesses. These businesses could be placed all across the country, or maybe beyond, and do legitimate business with everyday people, but their profits would help support Root. Also, on a rather amusing note, in the Sakura Hiden novel, the character of Kido Tsumiki is established, a man who actually was Root's treasurer. Even the bad guys have to manage books.

Other Things to Consider: Moving and Transferring Agents

Lets go back to the idea that Root was an official organization of the Hidden Leaf and at some point, Hiruzen ordered it to be disbanded. This disbandment, as I have repeatedly said, was only "official," as Danzo kept on going anyway. But if that order came down, what do you think would happen? What would Hiruzen expect to happen?

He may not always pay attention, but if he gives that sort of order, that means he's angry, and that makes him more likely to follow up. As I said in the previous part of this world building series, Hiruzen not making sure Root was finished can be mitigated with some trickery, but this is what you'd have to deal with.

For one, if Hiruzen ordered Root to be broken up, he’d expect to see an influx of shinobi into regular ANBU forces, perhaps even other departments. This forced transfer of Root agents could potentially expose those of them with forged graduation data, as seems to be the case with Sai and Torune, and maybe even Fu. 

Therefore, you’d need to think of a way to ensure those things don’t come to light. Danzo probably would have to transfer some of his agents, but he might not transfer all of them, lying about the full size of his forces. If Hiruzen had never seen the full size of Root’s forces, this lie could actually work. 

There's also the issue of moving. Root has their own HQ underneath Konoha, so wouldn't they be forced to literally pack their bags? What happens to their facilities once they're officially disbanded? Root can't still be using that space, can they? Konoha could just lock the doors, this is true. But they could also choose to take that same space and reuse it for something. It's a perfectly good workspace, so if they have a need, why let it go to waste, you know?

Once disbanded, Root would have to clear out any incriminating evidence before Konoha showed up, and either operate there in extreme secrecy, or just find a new hideout to use. Or perhaps Root did have other facilities that Hiruzen didn't know about in the first place. That is entirely possible as well, and they could have moved there.

Root and the Acquisition of Clan Children

Danzo has been described by some as power hungry, and he clearly wanted someone from the Yamanaka and Aburame clans in his ranks. He also told Shibi that every clan with secret techniques had sent a candidate, though this statement could be interpreted as a lie. Danzo is a very distrusting man, and I can see that distrust feeding into a need for power, to acquire the secrets of the clans so he can guard against potential betrayal. But I also want you to think for a moment about how that would work.

I remarked once already that I think kidnapping would probably work best for how characters like Fu and Torune were brought into Root. If Root is hidden in the first place, or if we're talking Root post-disbandment, this method would be the best one for any clan children in their ranks. But it would be more complicated than that. Age would matter. Why does Danzo want clan children in his ranks? Because they have powers. They have secret techniques that can be useful to him. However, not all secrets are equal.

With the Uchiha, picking a candidate for Root would be somewhat easier, as the Sharingan is built in. Kishimoto once said that if someone with a Sharingan and someone with a Byakugan had kids, those kids would have one of each.

That's co-dominance right there, meaning each dojutsu is a dominant genetic trait, meaning the vast majority of the clan members have it. Now consider the abilities of clans like the Yamanaka. They don't have a kekkei genkai, a genetic ability (though certain inherited traits found in the family may help).

Instead, their techniques are what's called "hiden jutsu," or secret techniques. These are jutsu that can be taught, with instructions and everything, and the clans work very hard to keep them in the family. Again, certain physiological traits found in the families may help facilitate the use of these techniques, but the point still stands that they have to be taught, not unlocked, and could also be taught to outsiders. What this also means is that Root agents from such families could only be "recruited" (read: shanghaied) at the right time.

If Fu had been brought to Root at say...four years old, the effort would be useless, as Fu wouldn't know a single thing about his clan's techniques. Danzo may prefer to target children, as they'd be easier for him to train, and to be fair, even if his target range was 10-12, those children probably wouldn't know much of their family techniques yet. They would, however, know something by that point, and that would still make them useful, providing a peek into the secrets of these great clans.

And that's all I have to say on Root. I hope you guys found this useful. Feel free to leave your own personal ideas and suggestions below. Now, if you excuse me, I'm going to go rest and then get back into full on fiction writing for a while.