Season 3

The team tries to deal with the possibility that Leo will not get better; a new mutant captures Raphael.

When the Turtles discover Bigfoot in the woods, Donnie befriends it and insists they protect it from a hunter.

When the guys discover a Kraang ship buried under April's house, they also uncover April's lost mother.

When he gets upset, Mikey flees and befriends a mutant frog in the woods, only to learn the frog and his family have nefarious plans.

When the Turtles are trapped in their dreams by creatures, April and Casey must figure out how to wake them up.

When Casey and Donatello bond while building Casey's new hot rod, the bond is challenged by a hot-rodding mutant.

When Casey, Raph, Mikey and Donnie are captured by a new mutant, April and Leo must overcome disabilities in order to save them.

Leo takes the Turtles to train in the woods in an advanced ninja ritual; the Turtles must overcome their weaknesses and face their enemies to become a true ninja.

When the Turtles return to the city to search for Splinter, they discover that the city has been overrun with Kraang.

As the Turtles search for Karai, they are forced to deal with a city filled with Kraangdroids as well as Zeck and Steranko.

Donnie finishes a new batch of retro-mutagen in hopes of saving Karai; the Turtles are hunted by Shredder's new henchmen, Bebop and Rocksteady.

Part 2

Casey Jones thinks he can take on the criminal underworld on his own, but soon discovers that he is in over his head.

A new and unfamiliar mutant known as Muckman begins to gain notoriety as New York City's "Monster Hero."

The Shredder kidnaps and experiments on the Mighty Mutanimals.

Michelangelo and Casey become friends with Mondo Gecko, a radical, skateboarding, reptilian teenager.

When Karai is brainwashed, she begins hunting the Turtles.

When the Turtles are whisked through time by apprentice Time Master Renet, they all must work together to defeat the evil Time Master Savanti Romero.

When the Turtles are accidentally transported to the past, they happen to cross paths with a familiar ninja clan.

After an accident, Donnie finds himself slowly losing his intelligence.

After being kidnapped by the hypnotized Karai, the Turtles are placed in deadly traps that they must work together in in order to escape. Splinter, in his efforts to save the turtles, is forced to face Karai in order to free her from Shredder's control.

Raphael meets a confused alien dinosaur named Zog, the Triceraton.

When the turtles get word of the Kraang's return, they realize there is an even bigger threat coming to Earth.

When the turtles get word of the Kraang's return, they realize there is an even bigger threat coming to Earth.