A team of archaeologists stumble upon a temple of unknown origin and culture buried near the Turtles' lair. However, before they can investigate further, they are frightened off by Baxter Fly, who explores the temple himself.
The Turtles hear about the discovery courtesy of April, not wanting their security to be compromised, the TMNT decide to investigate themselves. Shredder also has an interest in the temple; it contains within it a rare energy crystal, which could potentially re-power the Technodrome!
Baxter discovers the temple is actually a spacecraft with a sentient computer system at the helm, it is capable of accessing multiple dimensions, and Baxter plots a trap for Shredder and the Turtles. After The Turtles and Shredder meet up, Baxter springs his trap, using a muto-gun; he transforms Michelangelo into a baby turtle and Shredder into a fly (how ironic).
The TMNT are forced to team with Rocksteady and Bebop to battle and outwit Baxter.
They succeed and they restore Michelangelo