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.
The Turtles unwittingly release a wave of mutant squirrels on the city and must track them down before they threaten to destroy everything.
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.
The Turtles find themselves being hunted by a new threat--another mutant turtle called Slash, who has a personal vendetta against the brothers.
Raphael has to put his dislike of Casey Jones to work together against a common enemy.
Feeling left out of the action, April insists on joining the Turtles on a mission to TCRI, where they learn a shocking secret about April's past.
A fungus mutant spreading through the sewers causes the Turtles and April to experience their worst fears as Leonardo must face his greatest fear--losing his team.
When Donnie upgrades Metalhead's artificial intelligence, he must decide if he can trust a sentient Metalhead, or if he has created a new foe.
When the Rat King returns, Splinter must fight his fear to defeat his enemy. Also, April leaves Mikey with her new cat and it mutates into Ice Cream Kitty.
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.
When the Turtles play a fantasy LARP game to get their mind off of things, they must separate the difference between fantasy and reality.
The Turtles create a retro-mutagen to help April's father; Stockman-Fly kidnaps April.
Raphael is worried about Casey's ability to handle big mutant threats; Raphael and Casey cross the paths of Slash and his new partner.
Michaelangelo must battle Pizza Face in order to save his family.
Donnie becomes very jealous of April and Casey's relationship. April ends up being kidnapped by an evil spirit who wants to drain her powers.
The team visit the realm of Dimension X, Mikey is the only one to be able to figure the place out.