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The Clone Wars both make and destroy the 501st Legion. In is for them the same paradox that exists for all of the clones: they only exist because of the war, and yet the war destroys them. The 501st's casualty rates are some of the lowest in the Grand Army of the Republic, but the name of every brother who dies under his command still stays with Rex. He never quite gets used to the process: getting to know the new shinies, then watching them die, then waiting for the Kaminoans to ship out shines somehow even younger than before. But he always believes: when the war is over, we can fix this.
Rex learns the hard way that the 501st is lucky. They have General Skywalker, a skilled General, a General who cares about his men. After Krell, Skywalker is angry in a quiet sort of way. He’s furious at Krell, at the Council and General Kenobi for not noticing, and, Rex thinks, at himself. Skywalker works hard—harder than anyone gives him credit for, not even himself. He is a good man, and Rex will never stop believing that.
But here are things about Skywalker that make him uncomfortable. The man is a good General, but he’s far from perfect. He can be impatient—and impulsive. But the results are usually good enough to justify his methods. Usually.
He is also very close to the Supreme Chancellor. Rex doesn’t know the Chancellor personally, obviously, but he does read the Holonet on occasion, and he knows that the Chancellor and his allies have quietly prevented every bill on Clone Rights from having a vote on the floor of the Senate. He hears countless variations of: after the war, those things can be discussed—right now they’d just be a distraction.
And Rex does feel more than a little uncomfortable when Skywalker asks him to watch the door while he has a “private conversation” with Senator Amidala. He never says it’s Amidala, but Rex wasn’t born yesterday.
And after Commander Tano left, Skywalker had been very... upset. He’d given Rex a terse summary of what had happened at her trial, and then refused to discuss it any further. The men took her loss hard. Tano had been their Commander, but she had always seemed more approachable than Skywalker, especially to the younger men she befriended, more like one of the boys. But after she left, anytime the Commander’s name came up and Skywalker was in hearing range, his gaze became hard and cold. Brothers learned to not talk about her when the General was around. Rex had often wanted to ask about her, if Skywalker had heard any news. It felt a little like a betrayal that she never commed Rex to even tell him that she was alright, but he figured that Tano must have contacted Skywalker. But that was too much to ask for, he decided eventually.
If war teaches Rex anything, it's that he can't hold onto things. The brother who has been by your side since you both were tubies can just be gone one day, and you just have to keep on moving despite that. The only thing he lets himself hold onto is the belief that when the war is over, things will be different. He believes (or he has to believe) the promises the Republic makes to them about what will happen after the war, about back-pay and pensions, about opportunities for a fresh start for every brother who wanted one. A fresh start, like that brother on Saleucami had taken early. Rex thinks he would like something like that. All they have to do is win the war
(For a few moments, it looks like they will win—Dooku and Grievous dead, Maul captured. But by the time the war is over, Rex has lost nearly every friend he ever had. He watches the entire 332nd Company go down in flames. And all he can think as he buries his brothers is: we were so close, we were so close—)
The Clone Wars maim, scar and ultimately massacre the 501st. In the end, that is all the war was designed to be: the twisted machinations of a man who turned an entire galaxy to civil war in the pursuit of his own power, indifferent to the mass suffering he caused along the way. Palpatine was prepared—more than prepared, delighted—to burn the galaxy down and remake it in his image.
Palpatine uses the clones. He has never once thought of them as sentient beings, and it wouldn’t matter if he did. He has no qualms with using the lives of sentient beings to his own purposes as well. Palpatine betrays the clones, but in a way what Anakin Skywalker does to them is worse.
Anakin notices something is wrong when he orders his men to march on the Temple. Of course he does. In that moment, he is desperate and half-insane, but Anakin Skywalker has never been and never will be Force-blind. He sees the suffering of his men, the men he has fought beside for three years, the men who are his responsibility, the men he has come to care for, as their minds try and fail to fight against the control chip Anakin’s new Master had ordered installed inside their minds so many years ago. He does not know what is wrong, but he notices that something is not right, that the familiar minds of his men have been… altered, in some way.
If not the choice Anakin faced in Palpatine’s office, then this might be the last time Anakin might have turned back to the Light. But he sees the suffering of his men, sees that something is wrong with them, and Anakin chooses to look away. He has already condemned Obi-Wan, condemned the Jedi, condemned the Republic for his love. What are the souls of his men in comparison to that?
So often the galaxy has discarded the lives of the clones. Their General is hardly the first to do so, but for many of his men he will be the last.
General Skywalker marches on the Temple, his loyal troops behind him. He is their commanding officer, and like he has so many times before he leads his men into battle. He orders his men to gun down the old Masters and the too-young Knights and padawans defending their home, to gun down terrified children hiding under their beds. He barely even notices as his men are cut down by desperate and confused Jedi.
On that day, Anakin murders people who had respected him and trusted him, who had considered him a friend, a comrade. On that day, Anakin murders children who thought he was coming to save them. And he does it with his men by his side.
(When Anakin had been a boy, out of all the stories he heard in the slave quarters of Mos Espa, the ones that scared him the most were about control chips. According to the stories, some slavers had technology so advanced that it could even control a slave's mind. Not even their thoughts were their own.)
(Anakin’s body had never been his. But his mind had always been the one place where he could feel whatever he liked, where he could daydream about becoming a Jedi or finally winning a podrace, where he could silently taunt Watto. It made him sick with fear to imagine his mind not being his own. Anakin had slept in his mother’s bed that night, and Shmi had stroked his hair, assuring him the stories weren't true.)
Darth Vader is the Supreme Commander of the 501st Legion. From the countless clean-up battles after the end of the Clone Wars to the moment of his death in his son's arms at the end on the Second Death Star, he remains so. The small number of surviving clones are gradually phased out and forgotten, replaced with nat-born stormtroopers, but Vader stays.
According to the rumor mill of the Imperial Navy, something about the clones had seemed to irritate Lord Vader more than even the new stormtroopers. He was certainly more quick to enact his infamous “field punishments” on them. This lended credence to those among the Imperial Navy who believed Lord Vader to be a former Separatist who held some sort of resentment towards the clones, possibly even General Grievous reborn.
The Emperor laughs when his spies tell him about these rumors.
Most Imperials know better than to think Vader is the notorious droid general in a new suit. After all, despite his use of lightsabers, Grievous was not Force-sensitive. And Vader regularly demonstrated his talents with the Force, even if most surviving witnesses wished to forget what they had seen. No, most in the Imperial Navy knew that Vader is a Jedi. The only Jedi who remained loyal to the Emperor.
Of course, there was no way to know who exactly Vader was, if he really was a Jedi. There were thousands of Jedi who served in the war, and none of them were named Vader—but all GAR records were restricted after Palpatine declared the Empire, so who would really know if that was true?
And who would know, if Vader once, a year after the Clone Wars, accidentally called his new commander Rex? After all, Lord Vader would never leave alive any witnesses to such a humiliating mistake, if it did happen.
(If, after the Battle of Endor, the spirit of Anakin Skywalker notices an old veteran of the Clone Wars among the celebrating troops, an old clone who never stopped believing in his General, notices him sharing old memories of better times with his son, he says nothing.)