On their way to Saffron City, Ash and his friends encounter a Caterpie and its Trainer-in-training, Xander, who mistakes them for lab robbers. Fortunately, Dr. Gordon, the lab owner and Xander's teacher, shows up and things are sorted out. The kids visit Dr. Gordon's lab, where he makes all kinds of strange inventions. Of course, Team Rocket wants to steal them all!
Caterpie helps catch them in the act, but in the process, Dr. Gordon's briefcase opens and blue candies roll out. Caterpie eats some and grows until it's big enough to send Team Rocket blasting off. The Mystery Candy Complete keeps Caterpie growing until it's bigger than a building! The giant Caterpie heads into town as people flee in a panic. Climbing the local radio tower, it then evolves into Metapod.
Elsewhere, Team Rocket discovers that Wobbuffet stole some Mystery Candy too, so they head back into town and kidnap Dr. Gordon. The Candy makes Dustox and Cacnea huge—Dustox is so big that Team Rocket hops on its back and flies away with Dr. Gordon! Metapod evolves into a giant Butterfree just in time for Ash and Xander to give chase.
After some aerial maneuvers, Dustox suddenly shrinks back to normal size. Butterfree catches it but Team Rocket plummets into a pond. No sooner do they emerge than Officer Jenny arrives with Ash's friends, and when Team Rocket puts up a fight, Pikachu and Butterfree send them on their way once more. Eventually Butterfree returns to normal size too, and Ash says farewell to Xander and his newly-evolved friend—as well as Dr. Gordon, who's now more enthusiastic about his inventions than ever!