Karai searches for the legendary Kuro Kabuto, claiming to be the rightful heiress of the Foot Clan, when she suddenly encounters an old rival.
The Turtles believe they have defeated most of their old enemies, but they soon discover that a new evil is rising from the ashes.
The team must infiltrate Super Shredder's lair to finally end Oroku Saki for good.
Super Shredder has returned with even greater vengeance, forcing the Turtles to enlist the combined aid of Splinter, April, Casey, Karai, Shinigami and the Mighty Mutanimals to destroy him once and for all.moreless
A dangerous female mutant, by the name of Alopex, appears with a personal vendetta against Tiger Claw. The Turtles, April and Casey try to befriend her, but turns on them and furiously goes after Tiger Claw alone. Unfortunately for her, Tiger Claw has prepared for her unexpected arrival.moreless
Raph's bonding with little Chompy is interrupted by the invasion of Tokka, who has come to Earth searching for him.
When Donatello grows concerned about April, he decides to put her through a series of tests and learns that her psychic abilities are developing more rapidly and becoming more than he originally thought that they would.
The Turtle team hunts for their Sensei, but soon realizes they are being hunted as well.
The Turtles struggle as they battle the Super Shredder, who proves to be a formidable opponent.
Michelangelo befriends two odd looking superheroes named Wingnut and Screwloose.
Don Vizioso and his gang equip themselves with a number of anti-mutant weapons to use against the turtles.
Raphael must overcome his fear of insects when Baxtar Stockman creates an army of insect minions that have kidnapped Casey.
Leonardo teams up with Karai only to wind up in more danger than he realized.
April must face a deadly enemy while the turtles must deal with some old foes.
As the turtles finally make their way back to Earth, the Fugitoid tells them about a horrible secret from his past.
The turtles head to the planet known as Magdomar to try and locate the final piece of the Black Hole Generator.
When Mona Lisa asks for help from the Turtles, they become ensnared in Lord Dregg's trap, and must escape his homeworld.
Donatello starts to feel jealous of the Fugitoid's intelligence, but this is soon put to the test during an attack by the Triceratons.
The Turtles journey through the cosmic ocean of Varuna, where they must proves themselves worthy to Hiidalra. Hiidalra is an aquatic alien queen who holds the second piece of the black hole generator.
The Turtles must gain the trust of the Utrom Council in order to find the next piece of the black hole generator.
The turtles are captured and thrown into the Triceratons' battle area.
When microscopic aliens invade Mikey's mind, the Turtles have to chase them through the strange world of Mikey's subconscious.
The turtles find the location of the first piece to the black hole generator, which is found on a planet that starts to play with the turtles' emotions.
After a fight with the Triceratons, the turtles' ship crash lands on an icy planet where they are forced to work together with a group of bounty hunters called the Salamandarians.
The Turtles, April, & Casey learn from The Fugitoid that the Earth can still be saved, by traveling back in time to prevent it's destruction.
The Turtles' failure to stop the signal to the Triceraton armada leads to an all out war between the Kraang, Triceratons, and Earth.
Raphael manages to befriend a mysterious life form named Zog, but is unaware of his evil intentions.