A mysterious meteorite hurtling toward Earth nearly strikes the Legendary Pokémon Rayquaza, the guardian of the ozone layer. The meteorite crashes into a polar region, revealing two glowing, egg-shaped objects. From the purple egg, the alien Pokémon Deoxys regenerates and retrieves a green crystal. Rayquaza, viewing Deoxys as an intruder, descends to attack. Their fierce battle destroys a nearby research facility, and in the chaos, a young boy named Tory is traumatized by a panicked stampede of Pokémon fleeing the destruction. The fight ends when Rayquaza lands a point-blank Hyper Beam on Deoxys, seemingly destroying its body. The remaining purple crystal falls into the sea, while researchers take the green crystal back to the Hoenn region for study.

Four years later, Ash Ketchum, Pikachu, and his friends May, Brock, and Max arrive in the futuristic, high-tech city of LaRousse. The city is known for its advanced Battle Tower and automated robot assistants that patrol the streets. At the Battle Tower, Ash mistakes a lone, shy boy for a Pokémon Trainer and challenges two other trainers, Rafe and Sid, to a tag battle with the boy as his partner. This boy is Tory, the traumatized child from the polar incident. Still deeply afraid of all Pokémon, Tory is unable to command Ash’s Pokémon, and they lose the match. Embarrassed, Tory flees but stops to rescue a Minun trapped in an automated trash can, revealing the kind heart beneath his fear.

Meanwhile, the purple Deoxys has fully regenerated in the ocean and senses the location of its long-lost companion, the green crystal being studied in Professor Lund’s laboratory in LaRousse City. Deoxys arrives and begins to systematically remove the city’s inhabitants using copies of itself to search for its companion. The city’s security robots begin to malfunction, adding to the chaos. Just as Deoxys closes in on the lab, Rayquaza reappears, determined to finish its battle with the alien invader. Deoxys creates a powerful force field that disables the city’s power, and the two Legendary Pokémon clash once more, causing massive destruction.

Inside the lab, Pikachu, Minun, and Plusle work together to charge the generator, causing the green crystal to regenerate into a second, green-cored Deoxys. As the battle between the purple Deoxys and Rayquaza reaches its peak, the newly revived green Deoxys intervenes, transforming into its defensive form to shield Rayquaza from a fatal attack. When the city’s main robot becomes hostile and overwhelms Rayquaza, the twin Deoxys work together, forming shields to protect their former enemy. Realizing the Deoxys are not a threat, Rayquaza begins to fight alongside them against the rampaging robots.

With Ash’s encouragement, Tory overcomes his deep-seated fear of Pokémon to help shut down the malfunctioning robot network. After they succeed, Tory nearly falls from a great height while trying to save Plusle and Minun, but the green Deoxys swoops in to rescue him. Seeing that the Deoxys mean no harm, Rayquaza peacefully departs. The twin Deoxys create a beautiful aurora in the sky as a farewell to their new friends before leaving for an unknown destination. Having conquered his phobia, Tory bids farewell to Ash and his friends at the train station with a Plusle and Minun perched happily on his shoulders as the journey continues.