The Turtles believe they have defeated most of their old enemies, but they soon discover that a new evil is rising from the ashes.

Karai searches for the legendary Kuro Kabuto, claiming to be the rightful heiress of the Foot Clan, when she suddenly encounters an old rival.

Donnie's grudge with Don Vizioso threatens the Turtle's newest mission.

The Turtles must defeat the mighty demodragon Kavaxas to prevent him from destroying the world.

When Mona Lisa suddenly arrives on Earth, Raphael must get her and Bishop to work together to defeat an alien threat and save the Earth.

When Mona Lisa suddenly arrives on Earth, Raphael must get her and Bishop to work together to defeat an alien threat and save the Earth.

The Turtles are transported to an alternate dimension where they meet the rabbit samurai, Miyamoto Usagi.

Usagi leads the Turtles through a haunted forest where they encounter mischievous and dangerous spirits.

As they reach their destination, Usagi and the Turtles must help Kintaro fulfill his destiny.

When Splinter first mutates, he must learn to survive the life of a mutant on the run while also protecting four baby mutant turtles.

In an alternate, apocalyptic future that takes place fifty years later, all humans and most of the mutant population have been wiped out, due to an extremely powerful mutant explosion that had mysteriously occurred through unknown means. Only a weathered Raphael, who has most of his childhood memories lost to him, and Donatello (whose consciousness has been transferred into Metalhead) have been traveling throughout the Impossible Wasteland trying to save alive while being pursued by the Verminator and his bikers. Befriending a female meerkat warrior named Mira, the last of her tribe, who harbors the secret to "Paradise" and that she must find a wise turtle called "the Holy Chalupa".

Raphael, Donatello and Mira continue to be trapped by constant sandstorms throughout the desert, but are saved by none other than Chompy Picasso, whose physical self has grown considerably over the decades. On their way, they manage to find "the Holy Chalupa" who is, in truth, an elderly thin Michelangelo himself. He takes them to his home of pizza, where Ice Cream Kitty waits. While, the three Turtles are catching up and trying to accept the loss of their leader and eldest brother Leonardo, they are all attacked by Verminator Rex who abducts Mira but is followed by an angry Raphael.

Still trapped in "the Pit", Raphael manages to defeat his two opponents and is hailed as leader of both tribes by the crowd. Aided by Mira, Mikey and Chompy, they flee in search of "the Green Paradise", but they end up having to deal with Leonardo, who ended up having his body undergo a second mutation and his mind scarred by the mutagen bomb, and is now the evil leader of the Wasteland, Maximus Kong.

When Renet (Mikey's crush from the future) returns, the Turtles must help her stop Savanti Romero from unleashing an undead army on modern-day New York by traveling back in time.

Count Dracula is awakened, and turns Raphael into a vampire.

Savanti recruits Frankenstein's Monster and will soon unleash his creatures on the 21st Century.

When Renet and the Turtles return to a world run by monsters, they realize they have made the situation even worse.

The 1987 Shredder and Krang recruit the 2012 Bebop and Rocksteady, finding them better than their own incompetent counterparts.

The 2012 Ninja Turtles trains the 1987 Ninja Turtles in order to be ready for a dangerous mission to hunt down 1987 Shredder and Krang while April and Casey enlists Karai and Shinigami in order to track down Bebop and Rocksteady.

After discovering a treacherous scheme, the Turtles, along with April, Casey, Karai and Shinigami, enlists the Mighty Mutanimals in order to defeat Bebop and Rocksteady. Meanwhile the 1987 turtles are trained enough to take down 1987 Shredder and Krang.