Leonardo, tired of Raphael's constant criticism, lets his brother try his hand at leadership for a while. Meanwhile, Leonardo meets a beautiful and dangerous female ninja who tries to lure Leonardo to the dark side.
While breaking into the hostile environment of TCRI headquarters, the Turtles discover the true intent of the Kraang and resolve to stop the alien invasion once and for all.
Fed up with being humiliated by Fishface and Dogpound and defeated by the Turtles, Baxter Stockman seeks revenge by luring both parties into a deadly labyrinth.
While the Turtles are infiltrating an undersea Kraang base, the Foot Clan attempts to capture April, forcing her to fend for herself in a battle of wits against Karai.
When Shredder schemes to create a fearsome army of mutants, the Turtles have no choice but to rely on the help of the newest recruit to the Foot Clan: The Pulverizer!
Donatello breaks into a secret Kraang detention center in order to rescue Kirby O'Neil. But when he discovers they are trapped inside with a deadly mutant prisoner, he realizes that breaking in was the easy part.
When Shredder teams with the Kraang to receive a batch of mutagen, the Turtles' problems only get worse--even putting their friendship with April at stake.
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 escaping into the city.
When the Turtles face Shredder's newest threat, an army of Robot Foot Soldiers, Karai captures Leonardo and forces him to do battle with these new and improved ninjas that can adapt to his every move.
Donatello obsessively experiments with mutagen in a bid to find a cure for April's mutated father. Unfortunately this puts April in danger from a new threat--Mutagen Man!
Michelangelo is tired of being the "runt of the litter." But when he fools around with some mutagen, he gets a dangerous infection that is mutating out of control.
April tries to resume a normal teenage life, but when Karai starts hunting her again, April realizes she may have put her new friend Casey Jones in danger as well.