TMNT 2003: After Mousers destroy the turtles' home, they discover tunnels beneath it leading to genetically mutated humans — victims of Shredder's old experiments, kept alive only by the crystals the turtles found. The mutants beg the turtles to bring down Shredder so no one else suffers their fate. The turtles agree.
TMNT 2 Battle Nexus: A fight with the Foot Clan at Oroku Saki's tower ends with Master Splinter inexplicably vanishing. The chase leads to the T.C.R.I. building — a front for the Utroms, a brain-like alien species. The turtles are accidentally teleported across the galaxy, where they meet the Fugitoid, get caught in a war between the Triceratons and the Federation, and encounter an intergalactic bounty hunter named Slashuur who claims to know something about Hamato Yoshi. They return to Earth, where the Utroms reveal the full history of Ch'rell — a rogue Utrom who crashed on Earth in feudal Japan, escaped captivity, and has been posing as the Shredder ever since. Baxter Stockman sabotages a virtual reality machine during the revelation. The turtles defeat both versions of Shredder, Ch'rell is exposed, and they barely escape before a destruction device detonates.