Pokémon: Destiny Deoxys(2004)

Pocket Monsters Advanced Generation: Rekkuu no Houmonsha Deoxys

Satoshi and his friends travel to LaRousse, where they meet a boy named Tooi who is afraid of Pokemon due to an incident that happened four years earlier. Meanwhile, Deoxys, a Pokemon from space, has reappeared, putting a barrier around the city and kidnapping people. Rayquaza, a Pokemon that lives in the atmosphere, comes to fight it.

(Source: Anime News Network)