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.
Dissension between the Turtles leads to them being captured.
After getting in an accident, Donatello begins to slowly lose his intelligence.
Leonardo decides to enter Shredder's lair and rescue Karai on his own. But he may be in for a deadly surprise.
The Turtles are sent back in time to Japan, where they witness first hand the severed bond between Oroku Saki (Shredder) and Hamato Yoshi (Splinter).
The Turtles are sent on a mystical adventure at the hands of a mysterious time traveler named Renet.
When Karai is experimented on with Shredder's mind control serum, he orders her to eliminate Splinter, The Turtles, and their friends.
Mikey and Casey meet a skateboarding gecko who looks to befriend them. But is this new mutant all he says he is?
Slash and The Mutanimals are captured by The Shredder to test a newly created mind control serum on them.
A freak accident mutates a modern day citizen into a mutant known as Muckman.