Yoshi, a Japanese ninja master, relocates to New York where he gets four turtles. Following a mishap, Yoshi turns into a manlike rat and the Turtles are anthropomorphized. Yoshi, who is now called Splinter, teaches the Turtles ninjutsu and allows them to go into the outside world for the first time.
Having witnessed the kidnapping of Kirby and April O'Neil, the Turtles seek to find the kidnappers and save the O'Neils, whereupon they are forced to fight a ruthless gang and a mutant monster. As news of those events spread, Yoshi's former foe, the Shredder, resolves to finish him off.
When a local called Vic records a video of the Turtles fighting the Kraang, the Turtles try to recover that video, which proves to be a difficult mission as Vic gets on Raphael's nerves.
After his arrival in New York, the Shredder plans to make an attack on Splinter and the Turtles; meanwhile, as Michelangelo seeks to befriend more humans, he becomes friends with a renowned martial artist named Chris Bradford, who turns out to be hiding a shocking secret.
Despite Splinter's forbidding them from leaving the lair, the Turtles go out stealthily, whereupon they meet a mad scientist called Baxter Stockman, which leads to terrible consequences.
As Donatello gets fed up with the unsophisticated Bō-Staff they're using in their battles against the Kraang, who use more advanced technology, he decides to build a robot turtle, which he calls Metalhead.
As Donatello joins forces with April to look into the mysterious disappearance of Dr. Tyler Rockwell, they uncover shocking revelations about a dangerous mutant monkey with psychic powers.
As Leonardo wonders if he did the right thing when he showed the leader of the Purple Dragons gang mercy, Xever and his aides kidnap the owner of a noodle shop to force the Turtles to come out of their lair.
April's imprisoned father manages to send her a warning message, whereupon she sets out with the Turtles to rescue Kirby, learning that the Kraang will detonate a mutagen bomb in New York in the process.
As April monitors the Purple Dragons, she discovers that the Shredder intends to destroy the lair of the Turtles, who come face-to-face with Dogpound, the mutated Bradford, in an attempt to save their home.
After Leonardo and Raphael taunt Donatello and Michelangelo by claiming that they're less valuable to the team, Mikey and Donnie must show their mettle as the Turtles are divided into two teams to take on the Purple Dragons as well as Baxter Stockman's latest invention, the Mousers.
The Turtles come upon a mutant alligator, which Michelangelo looks after and calls Leatherhead. Moreover, they find out that the mutant is in possession of a powerful piece of equipment that belongs to the Kraang.
After acquiring the power to control rats, a new villain who calls himself the Rat King starts terrorizing the city as well as controlling Splinter's mind, forcing the Turtles to embark on a dangerous mission to foil his evil plan.
As Leonardo has enough of Raphael's brickbats, he allows him to be in charge of the team. Later on, when Leonardo encounters Karai, a female Foot Ninja, she attempts to get him to change sides.
When April's school project attracts the attention of the Kraang, about whom Karai tells the Shredder, the Turtles and the Kraang face off in a fierce battle in a Kraang research facility.
As the Turtles run into their first fan, a teenager who fights crime under the name The Pulverizer, they get disappointed as they discover that he has no fighting skills.
After the Turtles find their way into the unwelcoming HQ of the Techno Cosmic Research Institute, they make startling discoveries about the Kraang's real plan, which involves an extraterrestrial invasion, whereupon they decide to take action.
Seeking to monitor the Kraang in TCRI, Donatello uses his pet cockroach, but as it gets mutated by accident, turning into a giant monster, it tries to exact vengeance on Raphael for trying to destroy it before.
Baxter Stockman decides to exact vengeance on the Turtles as well as Dogpound and Fishface, who have been treating him badly, by tricking them into entering the Maze of Doom, which is basically a death trap.
As Karai discovers the extent of the threat posed by the Kraang and the extraterrestrial invasion they're planning, she attempts to join forces with the Turtles; however, things don't go as planned.
Upon learning of the Kraang's evil plot regarding the water on Earth, the Turtles sneak into an underwater Kraang base. Meanwhile, the Shredder learns a surprising fact about April and sends Karai to abduct her, whereupon the two face off in a fierce battle.
As the Turtles learn that the Shredder intends to build a powerful army made of mutant fighters, they are forced to team up with The Pulverizer, who has recently joined the Foot Clan.
A mutant wasp stings Leonardo, who gets infected by the wasp's venom and causes Raphael and Donatello to get infected as well. As Michelangelo is the last to get infected, he struggles to cure himself and his brothers from the terrible effect of the wasp's sting.
Trying to save Kirby O'Neil, Donatello sneaks into a Kraang detention center by himself, upon which he realizes that both his life and Kirby's are in jeopardy as he finds out that a dangerous mutant is also imprisoned in the center.
When the Turtles attack the TCRI as they discover that the Kraang intend to launch an invasion, an epic battle follows in which the Turtles struggle to thwart the Kraang's plot and close an extraterrestrial portal to prevent the arrival of the Technodrome, the Kraang's warship in Dimension X.
Following the Kraang's abduction of April, the Turtles attempt to enter the Technodrome to rescue her. Elsewhere, Splinter comes face-to-face with his archenemy, the Shredder, but he makes a shocking discovery about Karai.