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.

A Foot Soldier named Alpha-1 has his intelligence increased, but it results in a Foot Soldier rebellion against Shredder and Krang and the duo's exile from the Technodrome.