The four Ninja Turtles arrive in the city of New York to find the Foot Clan showing up to cause trouble. Once the streets are cleared, the turtles are told by April via T-Glass that Bebop is robbing the city’s bank. He’s armed with chainsaw explosive bombs and guns. The turtles will need teamwork to get past him. In the second mission, Rocksteady, Bebop’s partner, is destroying the subway system and has placed dynamite bombs with timers set to go off. The four brothers are prepared for the hammer-swinging Rocksteady; April communicates to them that Slash is hiding deep in the sewers. In the third mission, the turtles investigate while watching out for Slash who is throwing temper tantrums. Leo and company are directed to a construction site high up in the skyscrapers. Karai, the headstrong granddaughter of Shredder and Leonardo’s secret crush, has the explosives put in place and the turtles have no time to waste. The bombs are defused but Karai is more than ready for Leo, Mikey, Donnie and Raph. She fights against the Turtles but they manage to defeat her, forcing her to retreat via a jet-pack, which impresses Mikey.
Armaggon is the fifth boss up to no good; he’s waiting aimlessly for his next bite and has no patience when the turtles approach him. He’s defeated and another problem occurs when they meet with Wingnut. The turtles can not stop his speedy movements until Wingnut makes a mistake in pausing during certain patterns. Wingnut is finished off and General Krang is not impressed with the turtles for making it this far. General Krang learns his lesson the hard way as the previous bosses have and the brothers celebrate too early resulting in General Kraang becoming Mega Krang. The Turtles have to use robots with lasers to fire at Mega Krang; lastly, Shredder is annoyed at the failures his subordinates suffered and takes on the fight with the turtles himself. Shredder proves to be more than a challenge for the turtles but through teamwork and everything else they have experienced, the Turtles defeat Shredder and save New York City from the Foot Clan taking over.