A mysterious meteorite bearing two mysterious eggs crashes onto Earth. The purple egg regenerates into a Deoxys, who looks for the green one and unintentionally involves in a battle with Rayquaza who believes that they are enemies of Earth and descends from the ozone layer to protect the Earth against them. The battle threats to destroy a nearby high-tech city where Ash, Pikachu and friends are currently visiting, and they have to intervene to avoid regrettable consequences.