Leonardo, Raphael, Michelangelo, and Donatello face threats across three narrative episodes and a bonus Nightmare chapter. Episode One sends the turtles to New York City to repel a Triceraton invasion, rescuing friends Casey Jones and April O'Neil with aid from Professor Honeycutt—the Fugitoid—before dismantling Triceraton commander Zaranmon's war robot. Episode Two pits the brothers against swarms of Mousers deployed by Baxter Stockman, protecting a captured Master Splinter through high-speed hovercraft chases and battles against Bishop. Episode Three sees the Foot Clan fall one by one—Hun, Karai, and ultimately Oroku Saki in his empowered Mega Shredder form—culminating in a tribunal before the Utrom council that exiles Shredder's controller Scherel to a frozen world. The Nightmare chapter then gives each turtle their own dream gauntlet, unlocking Ultimate Turtle forms via gembu scrolls collected in Free Battle mode and leading to a final confrontation with Ultimate Drako.