Four ninja turtles, mutated by a mysterious alien substance, must rise up out of the sewers and defend their city against evil forces from both the past and present.
Leo stages a rescue for Karai against Splinter's wishes. While the mission is a success, Karai's knowledge of the truth makes her rush out to take her revenge on Shredder for killing her mother and lying to her for so long, leading to an unexpected turn of events.
The turtles engage in a difficult battle, as they make a desperate assault on TCRI to shut down the Kraang portal.
Leonardo considers asking Splinter for help while facing Shredder's new assassin; Donnie must put aside his rivalry with Casey in order to uncover a Kraang plot.
Donatello breaks into a secret Kraang detention center in order to rescue Kirby O'Neil, but ends up trapped inside with a deadly prisoner called the Newtralizer.
After encountering mutants and ninjas, Casey Jones decides to take on "pure evil" alone. When he meets Raphael, the two hot-headed fighters must put their dislike for each other aside and work together against a common foe.
When simultaneous threats from the Purple Dragons and Baxter Stockman’s mechanical Mousers force the Turtles to split into two groups, Donnie & Mikey must prove that their “B Team” is just as valuable as Leo & Raph’s “A Team.”
When the turtles play a Fantasy LARP game to get their minds off things, they separate the difference between fantasy and reality.
While the Turtles are infiltrating an undersea Kraang base, the Foot Clan attempts to capture April.
After witnessing the Kraang in action, Karai realizes the seriousness of the alien threat and proposes an alliance with the Turtles....unless the Shredder finds out.
The Turtles create a retro-mutagen to help April's father; Baxter Stockman threatens to mutate April.
While trying to foil a Kraang invasion plot, the Turtles are hunted by a giant cockroach.
The Turtles find themselves being hunted by a new threat -- another mutant turtle called Slash, who has a personal vendetta against the brothers.
While tracking mutagen, the Turtles bring a mutated squirrel back to the lair. When it starts multiplying, the Turtles must hunt the squirrel mutants and prevent them from escaping into the city.
Michaelangelo must fight his brothers when they fall under the control of a parasitic wasp.
When the turtles get word of the Kraang's return, they realize there is an even bigger threat coming to Earth.