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At the end of the 3rd season, Splinter asks Shredder for a truce to stop the alien Triceratons. Shredder agrees but at the end of the battle, Shredder kills Splinter. The turtles hold him one last time before they, Casey and April flee with Fugitoid, as he arrives at the very last moment in a spaceship as Earth is sucked into a black hole.
However, in "Showdown", during Shredder's battle with Splinter, he reveals that in the aftermath of the fight that caused Tang Shen's death, he took Splinter's daughter, Miwa, and raised her as Karai. He has told her that he is her biological father and it was Splinter who killed her mother, as she has sworn revenge ever since.
Splinter seemingly defeats Shredder by sending him off the building right as the remaining Turtles arrive. All seems well until Leo looks on in horror as the Super Shredder gets back up and Splinter turns around in horror. Shredder stabs Splinter through his front, much to Raph and April's horror.
The turtles try to stop Kraang from rising the Technodrome but fail and the Triceratons destroy it with Kraang Prime and Kraang Subprime in it, they then try to activate the black hole generator on Earth, the turtles join with allies and enemies to prevent Earth's destruction but Shredder betrays them and kills Splinter for revenge, uncaring ...
While their relationship with her is tense at first after she follows them to April's parents' farm, she ultimately gains their trust thanks to Leonardo vouching for her and bonds with Raphael. After Splinter kills Shredder and takes over the Foot Clan, she helps train the new recruits and forms a close friendship with Angel aka Nobody.
Danny asks Splinter what happened to Saki, and Splinter implies that Danny has been working for him. Shredder discovers Danny and realizes that the turtles have returned, ordering Splinter to be killed. Casey and Danny free Splinter and defeat Shredder's lieutenant Tatsu, before convincing the remaining Foot members of Shredder's manipulations.
Later, Shredder sends her to steal more resources from Krang and uses that to create Koya and Bludgeon: a mutant hawk and hammerhead shark. After Splinter kills Shredder in issue #50, Karai offers him her sword and the role of jonin (leader) of the Foot. He accepts and gives Karai permission to travel to Japan with select soldiers to study ...
This led to his dealings with the Kraang and ultimately placing his want to kill Splinter over his survival. He does succeed in killing Splinter during the Triceraton Invasion, but the Turtles travel back in time to save Earth and warn Splinter, foiling Shredder's attempt and resulting in him being mortally wounded.