A family secret is revealed when Lieutenant Kazou Saki of the Tokyo Metropolitan Police arrives from Japan to arrest his brother Oroku Saki, who turns out to be the Turtles' greatest enemy. Shredder and Krang manage to get the Technodrome out of Dimension X and back to Earth again, but Donatello re-programs it to crash in the Arctic.
Michaelangelo's strange dreams lead him to seek out Mondo Gecko, a lizard who was caught in the same ooze as the Turtles. Gecko eventually rebels against his boss, Mr. X, and his bombing campaign. Note: First Appearance of Mondo Gecko.
The Turtles train with the Ninja Tribunal to prevent the resurrection of the Shredder. But when Splinter and the Ancient One express serious doubts about trusting the Tribunal, the Turtles are confused. If they all agree on the goal, why the doubts? To explain the danger to the Turtles, Splinter and the Ancient One reveal the secret history of the Tribunal… including the true origin of the Shredder!
The Turtles and company continue their training under the Ninja Tribunal, learning to fight in the physical as well as mental and spiritual worlds. They’re going to need that knowledge, because the second artefact of the Shredder has been found, guarded by a horde of nasty Tengu demons that eat Acolytes for breakfast… literally!
When the city is hit with a sudden termite infestation, the only superhero who can help—Bugman—is too at peace with himself to aid the Turtles in defeating it. They also end up fighting a villain called the Swatter. Note: Like in the fourth season in the series Michaelangelo Meets Bugman
The Justice Force is expanding its ranks, and Mikey plans on joining up as Turtle Titan!, while Leo is more concerned in alerting them to the threat of the original Shredder. But when Nano reappears (thanks to Bishop and Baxter Stockman), everything quickly spirals out of control into a super hero vs. nanotech slugfest! But has Nano come back as friend or foe? And will the Turtle Titan and Leo survive long enough to find out?
The original Shredder is resurrected by the Foot Mystics, whose first agenda is to destroy Karai – the “false Shredder.” And, while the Turtles are enemies of both Shredders, they realize that if the original Shredder wins, his goal of creating a world of destruction, devastation and chaos will be one huge step closer to reality. So, like it or not, they have to help Karai – even while she’s intent on killing them!
In their attempt to rescue Karai from the Foot Mystics and new Shredder, the Turtles wind up in a raging battle filled with magic and martial arts where they use everything the Tribunal taught them - but will it be enough to escape with Karai and their lives?
Baxter Stockman leads a swarm of flies in an attempt to conquer New York and prove his worth to Shredder and Krang so he can become human again. Title Reference: Lord of the Flies Note #1: Like in the fourth season in the series "Son of Return of the Fly II" Note #1 : He will also return in the seventh season in the last appearance of the series "Revenge of the Fly".
Tired of fixing everything in the lair, Donatello decides to clone himself so he can work on his other inventions. However, Donatello's clone turns against him and joins the Rat King in an attempt to conquer the city with a rat infestation.
Bebop and Rocksteady botch another mutagen experiment, resulting in a giant ice creature who Bebop dubs "Frosty", and Shredder uses this monster to freeze New York solid, preoccupying the Turtles long enough for him to steal thermal explosives needed to melt the Technodrome free from the ice. Title Reference: The Iceman Cometh
With the help of their closest allies and most dangerous enemies alike, the Turtles have fought their way through a demonic version of New York to confront the Shredder once and for all! Now the Turtles must have everything they've got and have no choice but to focus their energy and become their very own mystic avatars...Dragons. This night, the Teenage Mutant Ninja Turtles will meet their destinies: Whether to live or die!