Teenage Mutant Ninja Turtles' second season originally aired between November 8, 2003 and October 2, 2004, beginning with the "Turtles in Space, Part 1: The Fugitoid" episode. The episodes were first released on DVD in eight volumes, TMNT Volume nine through Volume fourteen. The volumes were released From May 18, 2004 through January 18, 2005. The episodes were later released in 2 part season sets; part 1 was released on February 19, 2008, containing the first 12 episodes of the season, and part 2 was released on October 28, 2008 with the final 14 episodes.
Picking up from the previous season's cliffhanger, the Turtles find themselves teleported to the alien world of D'Hoonibb, where they immediately are caught up in a war between the Triceraton Republic and the Galactic Federation. The two races are fighting over Professor Honeycutt, who has the plans for a teleportation device that both sides seek for their war efforts against each other. The Turtles end up on the Triceraton home world, and after saving Honeycutt, are teleported back to Earth by the Utroms. The aliens reveal themselves to be benevolent and reunite the Turtles with Splinter, who they had healed after their last confrontation with the Shredder, who survived the battle as well. His attack is foiled when the Utroms are able to teleport to their home planet with Honeycutt, and his true nature as an Utrom criminal named Ch'rell is revealed before he is defeated once again.
In the wake of the Shredder's defeat, a gang war erupts over control of his lost territory by the remainder of the Foot Clan, Hun and the Purple Dragons, and the New York mafia, aided by Baxter Stockman. The Turtles argue over their place in fighting in the war, but end up aiding Karai, the Shredder's adopted daughter, in claiming control of the New York Foot Clan and restoring order to the city. Though they part with a friendly ceasefire, the Shredder is revealed to have survived yet again, and Karai's loyalty to her father conflicting with her honor becomes a critical dilemma for her for the remainder of the series.
In the season finale, the Turtles follow Splinter to the Battle Nexus, a kingdom where a tournament is held between the multiverse's greatest warriors by the Ultimate Daimyo. The Turtles meet new allies in the form of Miyamoto Usagi and Murakami Gennosuke, and end up working to defeat an attempted coup on the Daimyo's life by his own son and Drako, an old foe of Splinter's.