Later in the third season, Stockman reappeared in "Bye, Bye, Fly," eking out a miserable living in the catacombs beneath the city, feeding off trash. As the episode began, he stumbled across a group of archaeologists, who had unearthed what appeared to be an ancient temple beneath the city. Enraged that his catacombs had been invaded, Stockman chased the archaeologists out and investigated the temple, which, in actuality, turned out to be an interdimensional space ship that had crashed on Earth centuries ago. The ship's sentient computer was happy to have some company at last and befriended Stockman, providing him with a trans-mutation gun that allowed him to have his revenge on Shredder by transforming him into an ordinary housefly. Stockman also used the gun on Michaelangelo, turning the Ninja Turtle into a pet gerbil, but Mikey's brothers managed to save the day and return him to his regular reptilian state. The Turtles escaped the ship just before it took off for Dimension X, taking with them a key component of the ship's warp drive, without which the ship disintegrated in mid-flight, stranding Stockman in interdimensional limbo, with a giant alien spider bearing down on him.