A mysterious meteorite is hurtling towards the earth. During its entry into the atmosphere, it almost wounds Rayquaza, a sky guardian living in the ozone layer. The meteorite crashes into a polar zone, revealing two egg-shaped objects. The purple egg regenerates into a Deoxys and picks up the green egg. Rayquaza descends from the ozone layer to fight the invader (believing it to be an enemy). A battle ensues, destroying a nearby research site and traumatizing a young boy Tory (Tou’i), scared by a stampede of Spheal, Sealeo, and Walrein. Deoxys engages Rayquaza and the two take turns delivering devastating blows to each other, but the fight draws to a conclusion when Rayquaza surprises the alien Pokémon and fires a point blank Hyper Beam at it. Deoxys’ body is destroyed, leaving only the purple crystal in its chest that falls into the sea, while some researchers take a similar green crystal that it found with them to Hoenn. Beneath the sea, the injured Deoxys regenerates and waits.
Four years later, Ash, May, Brock, and Max travel to LaRousse City, where block robots patrol the area. There they meet Tory, who has since become afraid of Pokémon and a loner. Deoxys, which has fully healed, leaves to find the green crystal which Tory’s parents are testing in a lab.