The story follows Ash Ketchum and his friends in Larousse City, a high-tech metropolis. Their visit is interrupted by a meteor crash landing nearby, carrying the alien Pokémon Deoxys. Deoxys, confused and angry, disrupts the city's technology and creates havoc.

Meanwhile, a young boy named Tory, who has a fear of Pokémon, is caught in the chaos alongside Ash and his companions. As Deoxys unleashes its power, the legendary Pokémon Rayquaza emerges to defend its territory.