The Ninja Turtles are on the run and are alone; Leonardo is a leader who is without anyone to lead; Leo has to stop Bishop and her Mechazoids while trying to save his brothers.
To save his brothers, Mikey needs the help of Bishop's intern, Rod; but Rod wants something in return; he wants to be turned into a mutant.
Raph's strength won't save him when he's caught between the Mechazoids and the notorious street gang known as Purple Dragons; Raph's going to have to use his head to get out.
It's a battle of the wits between Donnie and Bishop as he races through NYC's subway system to stop her evil Mechazoids; discovering how do you beat an AI that counters every move.
The origin of the woman called BISHOP! Why does she hate mutants? What is the secret of the Mechazoids? And exactly what happened the night the Turtles fell into Bishop's trap?
The Turtles take the fight to Bishop but she's ready for them; the Mechazoids go out of control.
The Turtles and Mutanimals are caught in the storm of the century; when a new group of sea mutants threaten the city, Raph will be forced to use his words to save the day.
Mikey and Genghis Frog are sent into the storm on a supply run to the local market when they encounter the electrifying Lee The Eeel; now Mikey has to step up and be a leader.
When the Lair floods, April goes to save Splinter, but he won't leave the sewer; to make matters worse, the mutant called Goldfin comes with a warning of staying out of his way, or else.
Donnie and Wingnut go to restore power to the Lair but get trapped by the East River 3; the water is rising and they're not alone, there's a monster down there with them.
The mutant seahorse called Mustang Sally is going to flood the city and the only thing standing in his way are Leo and Pigeon Pete; being the leader isn't all what it's cracked up to be.
The East River 3 are on the verge on victory; The Turtles and Mutanimals must team up to stop them, but not everything is as it seems, they need to discover what is the pearl and why does Goldfin want it.
