After April receives a warning from her imprisoned father, she and the Turtles embark on a mission to save him and stop The Kraang from detonating a mutagen bomb in the city.

When simultaneous threats from the Purple Dragons and Baxter Stockman's mechanical Mousers force the Turtles to split into two groups, Donnie & Mikey must prove that their "B Team" is just as valuable as Leo & Raph's "A Team".