In Episode 1, the Turtles defend New York City against a Triceraton invasion, destroying their carrier ships and fighting their way through Central Park to rescue Casey Jones and April O'Neil. Triceraton commander Zaranmon deploys a robot to stop them; Traximus helps the Turtles push through.
Episode 2 sees Baxter Stockman's Mousers flooding the sewer and targeting Master Splinter with debilitating sonic attacks. Splinter is captured and taken away in a van. The Turtles give chase, fight through a pair of ambushers, and eventually face Bishop to rescue their sensei.
Episode 3 takes on the entire Foot Clan hierarchy — Hun, Karai, and finally Oroku Saki himself, who has been upgraded into Mega Shredder. After his defeat, the Utrom council convenes a tribunal: Ch'rell is exiled to a frozen planet, while Karai and her allies are handed over to authorities.
The Nightmare chapter assigns each Turtle a dream-world sequence with its own bosses. Clearing enough of these missions unlocks the final boss, Ultimate Drako, and the path to the Ultimate Turtle forms.