Deoxys first appeared in Pokémon Ranger - Deoxys' Crisis! (Part 1), where it emerged from a portal in the sky. As Max saw Deoxys, he experienced a vision of space as soon as it went back into a portal.
Later, Solana investigated a cave as it was the source of recent geomagnetic disturbances, but Ash and his friends ended up tagging along. At the end of the cave, Deoxys emerged from a portal above a meteorite that, according to Nurse Joy, fell ten years ago. Deoxys attacked Ash, his friends, and Solana several times. Solana tried capturing Deoxys with her Capture Styler, but her efforts failed as it had to be in Normal Forme. Max was able to sense Deoxys's feelings of pain, which Solana was able to confirm with her scanner and used a Miltank to heal Deoxys. Max climbed up the meteorite with Meowth and Deoxys up there. Deoxys created a Safeguard around itself, Max, and Meowth. Max soon learned that Deoxys felt cold and scared as it traversed through space. Deoxys then took the two to its world.
In Pokémon Ranger - Deoxys' Crisis! (Part 2), Deoxys continued telling Max its story. After Ash and the others returned to the cave, Deoxys came out of its world. Everyone evacuated the cave as the meteorite was overloading with energy while Deoxys went back in its dimension. Solana theorized that Deoxys emerged from the meteorite, its cradle, after solar winds hit the space rock. The resulting electromagnetic forces caused Deoxys pain, so it fled to its own world. Deoxys emerged from the portal with Max and Meowth still inside. The group battled Deoxys in an attempt for Solana to capture it, and this also allowed Meowth and Max to escape the alternate dimension. Sceptile battled Deoxys in order to get it to change into Normal Forme, and managed to do so. Immediately afterwards, Solana successfully used her Capture Styler to capture Deoxys. Solana had it use Recover to heal itself and then protect the group from the meteorite's strong blast of energy. With the disturbance gone, Deoxys left to continue exploring the world.