Some TMNT stuff really isn't for little kids.
While the element of Splinter originally being Hamato Yoshi is still present, Oroku Saki is now the Foot Clan's medieval leader, with Splinter and the Turtles being the reincarnations of the human ninja warrior Yoshi and his four beloved human sons. They were killed after Yoshi had openly criticized Saki's increasing hunger for power and bloodlust before the Foot Clan.
Centuries later, all five were reincarnated as laboratory test subjects at Baxter Stockman's StockGen, a bioengineering firm in New York City. Yoshi had been reborn as an ordinary rat who was allowed to run wild through the laboratory. Eventually a psychotropic compound that gave the cognitive characteristics of a person to an animal (or "splintering" the human-like cognition from the instinctual animal state, a term to which Splinter owes his name) was tested on Splinter, allowing him to remember who he was and recognize his sons, now reincarnated as baby turtles. When agents of the Foot Clan break into StockGen and attempt to steal an alien mutagen, Splinter and the Turtles were also picked up and nearly stolen. But Splinter was able to escape with his sons, who were dropped into a pool of mutagen and slipped away in the sewers, save for the second-eldest son, Raphael, who was lost in an alley due to Old Hob.
Splinter found himself mutated into a more human-like rat, with more human capabilities such as the power of speech. His sons Leonardo, Donatello and Michelangelo had likewise been mutated into humanoid turtles, and though they did not immediately remember their old life as he did, he taught them ninjutsu and emphasized the importance of their family bond. When they were ready, Splinter commanded them to find their brother Raphael in the streets, which they eventually succeeded in doing.
With their family reunited, Splinter found himself endangered by his old enemy, Hob. Not only did the mutant alley cat want revenge for his lost eye, but he had been tasked by Baxter Stockman to retrieve Splinter's blood, which held the untainted psychotropic compound. He was then kidnapped by the Foot Clan, and found himself face-to-face with his supernaturally-resurrected old enemy, Oroku Saki, now known as the Shredder.
Splinter suffered a more devastating loss in the "City Fall" arc, in which Leonardo was abducted by the Foot and magically warped into Shredder's chūnin (second-in-command). His eldest son's induced hatred for him hurt Splinter deeply, but he never stopped working to save Leonardo from his enemies. As Leonardo recovered from the brainwashing, Splinter told his son that he would never give up on him, because of his mother Tang Shen.
This fragile bond later became a source of vulnerability when the Rat King targeted Leonardo and Splinter, making them hallucinate that the other was trying to attack.
After Leonardo's brainwashing, Splinter's view of the threats to his family and the world narrowed considerably, as he became increasingly obsessed with stopping Shredder and the Foot, to the point of dismissing the threat of Krang and the Technodrome. To this end, he forged an uneasy alliance with Hob and even went so far as to steal mutagen for him. Leonardo and Donatello concocted an elaborate plan behind Splinter's back to forge a false alliance with Shredder, so that they could pit the evil ninja against the alien warlord.
Unfortunately this led to further heartbreak for Splinter, as Donatello was found nearly dead after the mission was completed, having been attacked by the Shredder's thug Rocksteady. Splinter entered the spirit realm to guide his son's soul back to the living world, even as Fugitoid tried to save his body. Before Donatello could be restored, flyborgs and M.O.U.S.E.R. robots attacked the family's abandoned church lair, repeatedly saying "Kill the rat." As they escaped, the family encountered Oroku Karai, who was displeased by the dishonorable method of using robots.
Splinter finally sought an end to the war between his family and the Foot, challenging Shredder to the Gauntlet, an ancient ritual that will pit Splinter and the Turtles against Shredder and four mutant champions. Splinter meditates during his sons' fights with the mutants and then with Shredder, seeking a way that would allow him to triumph. He is the victor in the battle that ensues, and serves as Shredder's second when his old enemy commits seppuku, striking the head from his shoulders.
Karai surprised everyone by offering Splinter leadership of the Foot Clan, and much to everyone's shock, he accepted the position. His goal was to remold the Foot into a more honorable, less bloodthirsty form, one which would not be a danger to his family, but he was unable to remain true to his moral convictions in doing so.
Splinter's leadership of the Foot Clan slowly but inexorably drove a wedge between himself and his sons. Michelangelo fled immediately, unable to live with his family while they were part of an organization like the Foot, much to Splinter's grief. And after the destruction of the Street Phantoms and Splinter's brutal execution of a defenseless Darius Dun, Splinter's other sons found that they also could not condone what he was doing, which he understood and agreed with, advising Leonardo that he would now have to be the head of their family, Clan Hamato.
Though Splinter was no longer living with or in regular contact with his sons, he still clearly loved them and was watching over them, as evidenced by his secret visit in the Christmas Special. He also put the resources of the Foot at their disposal, as evidenced by him providing transportation for Raphael and Angel Bridge to find Alopex.
The invasion of the Triceratons brought Splinter back into conflict with outside forces, as he saw the Triceratons as an imminent threat, and even went so far as to offer Agent Bishop a temporary alliance in order to deal with the problem. It also led to more conflict with the Turtles, as Splinter was determined to keep them safe at all costs, even if it meant imprisoning them or killing the Triceratons to avoid future conflict. The Turtles tried to convince him that they had a solution, but Splinter refused to listen to them, even engaging them in combat when they attempted to defend Commander Zom. However, he showed pride in Donatello's cleverness when the Triceratons were unexpectedly teleported away.
Despite Splinter's conflict with his sons, they never completely severed contact with him, and after both the Triceraton-Earth Protection Force war and a recent conflict with the Rat King, the turtles asked their otherwise estranged father to take in the children made homeless by the destruction of St. Robert's Orphanage. And while Splinter agreed to take in the children, the disagreement Splinter had with his sons about his decisions and methods remained unreconciled, and Splinter even openly regretted letting Leonardo succeed him as Clan Hamato leader. Most of the turtles were nevertheless inclined to come to a truce with Splinter, but Michelangelo strongly objected to Splinter's condition that the orphans must be trained as the next generation of Foot Ninja. Mikey tried to sneak the children away from his father's reach, but he was tracked down, and an unusually hostile Mikey vowed to oppose what his father had become and prevent Splinter from turning the orphans into weapons. Splinter angrily attacked his son, but Mikey steadfastly refused to yield, swearing he would sooner die. Splinter finally relented, agreeing to let the turtles (and only the turtles) teach ninjutsu to the orphans, promising that each of the orphans would later be given a free choice whether to join the Foot Clan. While both Splinter and Mikey managed to save face, the dispute left Splinter demoralized at becoming someone who gets angry and harms his sons.
Shortly after the events of "Battle Lines", Splinter spent a lonely Christmas Eve at the Foot Clan compound when he was visited by the spirit of Oroku Saki, who warned him that he was in danger of going down the same path. He was then visited by three members of the Pantheon: Aka, who showed him his past as a human; Toad Baron, who showed him the present Christmas Eve experienced by his sons; and Gothano, who showed him a dark future in which a cruel Splinter is slain by his sons. Taking this as a warning, Splinter dressed as Santa Claus and distributed gifts to the orphans, while summoning his friends and family to the compound to celebrate Christmas.
When Karai finally returned from Japan, she started a war of domination over the Foot Clan under the influence of the Kira no Ken (a cursed katana that had once belonged to Takeshi Tatsuo). In the end Karai won the war, but Splinter escaped from his captivity. At the same time, however, put the demigoddess Kitsune set out her plan to restore her father - the Dragon back to Earth in Oroku Saki's body.
At some point later Splinter appeared before Oroku Saki as his soul was traversing Hell. He brought him before The Dreamer, and explained how Saki was being used by the Dragon. After a short reunion with his wife, Splinter went after Saki to continue helping him, taking the form of a normal rat in doing so. In order to halt the Dragon's ascent into the earthly dimension, Saki had to be brought back to life; to make this possible, Splinter willingly gave his life in Saki's place but not before telling his sons, their friends, and allies that he loves them all and apologizes for his past wrongdoings. In the afterlife, he was reunited with his beloved Tang Shen, and the two entered eternity to be reborn into a new life together.
Following his funeral the Turtles entered a period of deep depression; while Donatello was for the most part driven to fix the rift caused by Splinter's passing Leonardo and Michelangelo entered a state of malaise and thus suffered while staying at April's farmhouse. Raphael for his part left the group and was a vigilante in Mutant Town for months, working alongside Apolex to protect the victims of Ray and Hob's Mutagen Bomb.
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- In issue #7: Enemies Old, Enemies New, part 3, Woody reveals that Splinter likes large antipasto salad with extra olives.
- The Annual 2012: Big Trouble in Little Italy, reveals that Splinter watches soap operas.