After his defeat (as Meta Ridley) in Metroid Prime and then his later defeat on Norion in Metroid Prime 3, he somehow manages to survive and live on.
Later, presumably when returning to the Phazon-altered Space Pirate Homeworld, he intakes large quantities of Phazon, turning into Omega Ridley. Even with this massive strength-increase, however, his long-time rival Samus Aran manages to later defeat him. His actual death, however, is technically not seen, and chronologically, he survives and reappears in Super Metroid with a pure organic body.
Metroid Prime 3: Corruption