Michelangelo befriends Leatherhead, an unstable mutant alligator who possesses a strange piece of Kraang technology, but the other Turtles aren’t sure whether Leatherhead is a friend or a foe.

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

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With the demise of their beloved father and Karai incapacitated, the Turtles, April, and Casey, infiltrate Super Shredder's new lair to put an end to Oroku Saki once and for all, no matter what it takes.

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

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

For the first time, the Turtles encounter something they cannot defeat – the Super Shredder!

Snakeweed returns and begins abducting people. Tired of Raphael's constant criticism while trying to stop Snakeweed, Leonardo lets Raphael try his hand at leadership. While away from the group, Leonardo meets a female Foot Ninja named Karai, who tries to lure him to the dark side.

Baxter Stockman seeks revenge on Fishface and Dogpound as well as the Turtles, and lures them all into a deadly labyrinth.

The Turtles face an army of robot foot soldiers; Karai captures Leonardo and forces him to do battle with ninjas that can adapt to his every move.

The Turtles are transported to another dimension where they meet their 1980s counterparts and work together to battle Krang.

The Turtles' plans to enjoy Halloween are put on hold when strange monsters threaten to transform New York City.

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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.

The Turtle team hunts for their Sensei, but soon realizes they are being hunted as well.

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

When Karai is brainwashed, she begins hunting the Turtles.

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.

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

Part 2

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.

The Turtles must brave the bizarre world of Dimension X to save the enslaved people of New York. Part 1

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

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When Leonardo secretly allies himself with Karai, he gets himself into deeper danger than he could have realized.