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Mikey was kidnapped by the Shredder and imprisioned in Japan, below a big traditional house in the middle of the open fields, a small dungeon like space was set up, Mikey was chained up and a tortured for many weeks, nearly months, where he was forced into obedience and submission before being left to die as Shredder went back to New York to "take care of some business", leaving Michelangelo in a deprivable state, mentally, emotionally, you name it, that cruel monster really just abbandoned a shattered soul alone on purpose so that he would die of starvation or something.
During his time locked inside that mansion, Mikey was close to completelly losing his sense of self, so in fear of forgetting his identity, he found himself a few sheets of paper and made somethinglike a diary, where he wrote about everything he still knew about himself, his name, his family and friends, his experience under captive, but not much.
The things he wrote about himself, it was just his name, his position as the younger brother, and what he remembered of his personality before getting conditioned into the facade of a voiceless servant, like his cheerfulness and unconditional love towards his family and friends, he writes about his wish that everyone he knows could just be like a big happy family, including his talent for cooking that could use some improving, as for what he documented about his family and friends, he wrote a deep description of them, what they were like, what they looked like, how he viewed them as, and most importantly, who they were.
Days kept going by, and he felt the isolation getting to him, also hunger, the house had current water flowing but food was limited and he was quickly running out it, he knew he couldn't just go out to get more, he was forbidden to leave, and he knew humans weren't going to take his appearance kindly, it could be a death sentence right away, the risk was too much to take, so he couldn't scape, even if he found a way how, since each and every entrance or exit was either locked or tightly blocked with furniture that Mikey had no strenght to move at that time.
The days turned into weeks and Michelangelo was slowly going insane, his mind was slipping away, it was terrifying, but his brain was too numb to actually react, and as he suffered, someone watched over him in heaven, a kind woman's soul, Tang Shen, Splinter's deceased wife, she watched over the family her husband build and was heartbroken to see them suffering, specially Michelangelo, she saw him being tortured, starved, subdued and abbandoned, by Saki, the man she once loved, the brother of her husband, she nearly left Splinter at one point to leave with him, but she refused, since then, Saki had became more of a monster than ever, commiting mistake after mistake while burning the bridges to return to his senses.
She was fed up with all the evil her brother-in-law was causing, first, he killed her, then raised her daughter on his devilish ways, not to mention the many times he tried to destroy the entire world, and now... he was heartless enough to torment the poor and pure soul of a defenseless teenager, just so in the end he would leave the turtle to rot and die alone, the heartache she felt was too much to bare and she prayed for Michelangelo, shedding tears as she did so, her sadness caused a heavy rain to pour down, the heavens heard her plea, as one of her tear streamed down her cheek, it fell onto the mortal realm in the form of a shiny and blessed rain drop, the tear fell near the house where Michelangelo was being kept in, right on top of a small mushroom, it's blessed properties made it grow into a large bush of purpleish glowy mushrooms.
The bush let out a sweet perfume that made it's way to the main house, it was a matter of minutes before Michelangelo caught up to the scent, it smelled so good that it was enough to make his stomach rumble, reminding him of his immense hunger, he curled up into a ball in agony and picked up the bit of strenght he still had to move forward, he arrived to the door to the backyard, it was where the perfume was coming from, he saw that the door was locked, but there was nothing on the way, he thought to himself a bit before acting out, but the despair of hunger was stronger and he went on with whatever the first idea he could come up with during his panic, so he backed off as much as he could and ran into the door as hard as possible.
The impact broke down the door and he bursted his way outside, being met with the cold touch of the rain drops on his green skin, he looked around aimlessly searching the source of that delicious smell, until his eyes met the bush of mushrooms, it glimmered the dark cloudy yard with a soft and tender lilac light, Mikey then felt like if the fungus was calling out his name, inviting him out, he walks to the plant and pats the mushroom heads with his finger, the sickening smell drives him mad and he gently picks a mushroom into his hand, he stares at it for a moment until he brings it to his mouth and eats it, it tasted good... so good... it felt like his hunger suddenly disappeared, Mikey was feeling satisfied and oddly relaxed, that was until he started getting really sleepy, he struggled to make his way back inside the house just to pass out on the corridor.
When Mikey woke up, he had no memory whatsoever, his mind was wiped clean and he now had no idea of who he was or anything at all, he became an empty shell, just a husk that something once lived inside, with not much to go off of, he explored the house, discovering it's wonders once again until he stumbles across his own room, where he finds the notes he made about everything, he learned that he had a family, friends and the cruel fate he met not so long ago, it was confusing but Mikey was able to pick up on the info just fine, the knowledge on those sheets of paper filled the mental void in his mind and spirit and he set out to "make his dream come true", because his mind distorted the messages left behind by his former self, he know believes that everyone in those scriptions are meant to be a family and that HE is the one that shall make it happen, no matter the cost.
Shredder eventually returns expecting to see a dead turtle on his basement, but instead, he was welcomed by Michelangelo, he wore a servant's robe and he greeted him formally before taking him to the dinnertable with a single meal set for him, Saki was convinced he had made a successful brainwash on Michelangelo, making him believe that Mikey was just adapted to his current position and was acting accordingly, so he sat on his chair and ate the food, it tasted decent enough, he was satisfied but as he tried to leave, he felt dizzy and disoriented, he stumbled around for a bit before falling on the floor unconscious, the last thing he saw was Michelangelo staring at him through the door, he had that indifferent and twisted smile on his face, and with that, everything went black.
When Oroku-sama woke up again, he was a new man, with no memories of his past self and ready to be rebuilt as a good man, and Mikey took that chance heads on, he misguided Saki by telling him he's a respectful and peaceful man that is the main source of income to the house, Saki Hamato (how Mikey named him) then began working on himself, going outside to buy food and all the necessities of life, he became quite known in the community as "the scary man with a golden heart".
Meanwhile, back in New York, Karai, the turtles and Splinter noticed Shredder's absence, Karai heard he was going out but he was very past the date he said he would return, and so, they decide to dig deeper into the matter, invading the Foot clan's HQ and finding the database through Karai, where they find out not only his location, but also find out that Mikey was in there, finally discovering where their youngest sibling was being kept prisoner, it was a matter of time until they found a way to go to Japan to rescue Michelangelo, once they arrive, they head inside through the backyard, they hide amongs the surroundings until they see Michelangelo, just casually standing by the door while watching the sky, his family immediately notices the many scars he carried, Mikey even managed to see them in a distance, making him smile and turn away, heading inside the house and making his whole family panic as they all rushed inside, he led them to the again empty dinnertable with meals set for all of them while Mikey sat on the head of the table.
It was sinister and very off-putting, but master Splinter stepped forward and sat down at the spot Michelangelo instructed him to, believing that this play house was some sort of cooping mechanism being taken too far, so he complies in order to apeace his son's troubled mind, Leo, Raph, Donnie and Karai all follow along with their father and sat down accordingly to Mikey's demands, Leo personally can't not notice his little brother's face, specially his eyes, they look lifeless and devoid of any light, the black of his pupils seems to have blended with his baby blues eyes turning it into a deep blue that resembles the depths of the ocean at night, truly terrifying for someone like Michelangelo, they all look at their meals confusedly and start eating it, still confused about what to do in this sittuation, they all adore the flavor, it was positively unusual, that's until they began feeling ill.
Leo was the first one to faint, falling on his face on top of the table, and then Raph fell back onto the chair and drifted to a deep slumber, then Karai tried to get away but passed out soon later and fell on the floor, same for Donnie who managed to get to the door but fainted before he could even open it, Splinter was horrified, he watched his kids pass out one by one without even knowing the reason, he passed out over the table just like Leo, his hand was still trying to reach out to his unconscious sons, they all woke up around the same time, and Mikey would take them come over for private talks, that were mostly just doctrination from Mikey's mouth to teach them about who they were and to get them all on the right track, at least to him, they all became brand new people, all formed by Michelangelo, who became the head of the family soon after.
Saki-san soon arrived, being welcomed by Michelangelo, his nephew, as usual, he then introduced his uncle to his brother's (Splinter's) family, as well as Karai, that according to Michelangelo, was his adoptive daughter, being originally Yoshi's daughter until he allowed Saki to adopt her, why would he do that? Because Yoshi felt bad that his brother never had kids of his own, and in traditional Japanese culture, children were really important for the whole family.
The family was soon united, and like that they stayed for a long time, an "ideal family", even with or without "yokais"(mutants), that was until April O'Neil showed up, looking for her friends, just like them, Michelangelo was waiting for her at the door, she was brought into the house and was met with the spine chilling sight, the turtles, master Splinter, Karai and the Shredder himself, all sitting on a dinnertable together, calmly and happily having dinner together, it felt twisted to see, but she was pressured to join in, no need to say, she ate the odd soup and eventually became part of the family of puppets as a "family friend".
But what Michelangelo didn't know about, was that she came with someone else, someone he didn't know of, at least from his old notes, Casey Jones, the little punk dude that followed April along to help her get their friends back, he watched from the shadows what happened and put the pieces together, his friends were all converted into... something like cult members, with no real mind of their own, he didn't know what to do, he had no idea, but his friends mattered more, even if he can save them, as the old saying goes "If you can't beat them, join them." and so, that's what he did, he turned himself in, Michelangelo didn't know who he was, but something about that guy felt familiar, so he let him in.
As Mikey gave Casey the mushroom stew, Casey was quite scared at first, but he wanted to be with his friends over all, he and Mikey shared one last chat before it all, the boy didn't have much to say, other than
"Thanks for letting me join you guys, I see you care for everyone a lot... great job, Mikey..."
That phrase, made something break inside Michelangelo, it triggered something, but when Mikey turned back to him, he was already drinking from the bowl, Michelangelo was very upset for some reason, a pinch of regret in his heart, but he didn't know what it was, so he just swallowed his feelings and moved on, accepting Casey in the family.
Some other plots that would go down could be:
*April having insecurities about her red hair and dying it black to match Karai.
*Leonardo, Raphael and Donatello wondering what is like across the fenced walls of their large backyard.
*Karai, Casey and April going out to the city with their "Uncle Saki".
*April and Casey learning Japanese.
*Michelangelo slowly regaining his memories after a few years.
*Saki becomes ill and passes away not so long after Casey joins the family.
*Karai becomes the main source of income for the house as the eldest child of the family.