The third season of Teenage Mutant Ninja Turtles originally aired between October 9, 2004, and April 23, 2005, beginning with the "Space Invaders, Part 1" episode.
Having observed the damage that has been done to Earth from the sidelines, Shredder uses his Oroku Saki persona to help in the reconstruction of New York, secretly salvaging Triceraton technology for an unknown purpose, while Bishop schemes to create an army of super-soldiers.
With Usagi's help, Leo travels to the Battle Nexus and is able to reunite his brothers and Splinter and defeat Ultimate Drako.
Bishop also enters the fray with Stockman on his side, but Shredder is able to lift off with Karai and Dr. Chaplin, with the Turtles and Splinter stowing away.
Fortunately, the Utroms arrive just in time to save them all and find the Shredder guilty of numerous war crimes and atrocities, banishing him forever to a desolate ice asteroid.