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.

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.

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.

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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.

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.

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

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

Part 2

Usagi and the turtles must help Kintaro fulfill his destiny as they reach the end of their journey.

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.

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

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

The Shredder kidnaps and experiments on the Mighty Mutanimals.

: The Turtles are transported to an alternate dimension, where they befriend the rabbit samurai and master swordsman: Miyamoto Usagi.

The Turtles, their 1987 counterparts, April and the Mighty Mutanimals must work together to stop 80s' Shredder and Krang from destroying the world. Meanwhile, Bebop and Rocksteady are faced with a difficult and life-changing decision.

When Shredder plans to create an army of mutants, the Turtles must rely on the help of the Pulverizer, who was recruited into the Foot (to be expendable) and volunteers to gather information on the inside on their behalf. When he agrees to be a test subject for a stolen supply of Kraang Mutagen, the Turtles rescue him, but not before he recklessly gets himself mutated.

The Turtles discover that the Kraang survived their previous showdown and have dropped mutagen canisters all over New York City.