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In Pokespe two Deoxys exist. They both mutated from a space virus at the same time and hitched a ride down to Earth on the same meteorite, where they were caught by Team Rocket. Deoxys 2 escaped and absorbed a sample of Red's blood, thus coming to think that Red was its sibling, having a magnetic-like pull towards the trainer. Team Rocket thus used Deoxys 1 to attack Red and stir up Deoxys 2, who would develop further through its battles with Red. Giovanni intended for Deoxys 2 to grow to a state where it could identify anyone, and so he could use it to find his long-lost son, Silver, at the same time taking revenge on Red for his constant defeats.
Deoxys 1 was "disposed of" after its use was complete. However, it survived, and escaped to space. There it found the largest meteor it could, and dragged it towards Earth as revenge for humanity trying to kill it. Eventually this meteor and this Deoxys were defeated by Mega Rayquaza's Dragon Ascent in the Delta Episode arc, with Ruby and Sapphire riding Mega Fug. Giovanni recognized this Deoxys as the one he threw away, but escaped any consequences for doing so.
