Splinter allows the Turtles to visit the surface for the first time, where they attempt to stop a group of thugs from kidnapping April O’Neil and her parents. But the Turtles, who have never been in actual combat before, fail miserably. Splinter, realizing that the Turtles need a leader, assigns the task to Leonardo. After some initial resistance, especially from Raphael, Leonardo’s leadership skills begin to take shape. The Turtles track down Snake, one of the kidnappers, and when they come upon a mysterious canister of mutagen (the same kind of mutagen that transformed the Turtles and Splinter 15 years ago) they realize this mystery is much bigger than they ever imagined...
Raphael loses his temper when he is insulted by a caustic New Yorker (Vic). The ensuing yelling match results in the Turtles being ambushed by the Kraang and blowing their mission. Worse, Vic caught the whole thing on video, thus raising the frightening possibility of the existence of the Turtles becoming widely known. Raphael must learn to control his rage and endure insults in order to help the others retrieve the video before it falls into the wrong hands.
The Rat King threatens to take control of the city and also Splinter's mind.
Raphael takes charge of the crew while Leonardo gets acquainted with a dangerous female ninja.
The turtles visit high school when April's latest school project peaks the interest of the Kraang.
The turtles encounter their fist devoted fan: a teenage crimefighter called "The Pulverizer."
A huge, powerful cockroach pursues the turtles as they attempt to sabotage a Kraag invasion scheme.
A vengeful Baxter Stockman sets up a dangerous maze and lures the turtles, Fishface and Dogpound to it.
Karai wants an alliance with the turtles, hoping their combined strength can defeat the Kraang.
The Foot Clan attempt to abduct April, who must try to outsmart Karai on her own while the turtles are on an undersea operation.
The pulverizer joins the foot and he voulenteers to be tested with mutagen and turns into a huge blob.Donnie and the others rescue him and keep them in the sewers.
When his brothers fall under the control of a parasitic wasp, Michelangelo has to fight them.