[2] Picking up from the first 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.
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, the Purple Dragons (led by Hun), and the New York mafia (aided by Baxter Stockman).
Leonardo and Raphael argue over their place in fighting in the war, but the Turtles end up aiding Karai, the Shredder's adopted daughter, in claiming control of the New York Foot Clan and restoring order to the city.
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, Splinter's old foe.