Some TMNT stuff really isn't for little kids.
The IDW Comics series which began in 2011 presents a new origin for both Splinter and the Turtles. While the element of Splinter 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 corporation, 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 drug that gave the cognitive characteristics of a person to an animal (or "splintering" the human-like cognition from the instinctual animal state, a term that 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-youngest 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.
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.