Splinter has suddenly disappeared, and a note left behind from him forces the Turtles to go their separate ways, but one by one, they are captured by Leatherhead and the Rat King.

While trying to contact the Turtle Nebula, Donatello meets an intelligent lizard alien named Algernon ("Algae" for short), who must help him and the other Turtles rescue April from a greedy man named Hostile Hiram Grelch.