After Gilmore beat Omega by proving his scientific theory, Omega began plotting a way to get back at Dr. Gilmore. He found a boy named Naku and converted him into Cyborg X. Omega then sent X to deliver a TV Screen to Dr. Gilmore, and used the screen to issue a challenge to Dr. Gilmore to prove whose Cyborgs were better. Omega also planted a Cobalt Bomb somewhere in Tokyo and threatened to detonate it if Gilmore refused his challenge.
After X brought a captured 003 back to Omega's island base, Omega shocked him for thinking about his girlfriend Michi and not fighting 009.
Cyborg 009 later fought Cyborg X, but during the fight, X accidentally fatally wounded Michi. Turning his attention away from 009, X freed Cyborgs 003 and 007 (who had also been captured) and grabbed the Cobalt Bomb with his ship. He then flew into Omega's base, causing the bomb to detonate and destroy both himself and the evil scientist.
- Omega is similar to Dr. Gaia in the manga and 2001 Cyborg 009 anime, as both are scientists who seek to seek to prove the superiority of their cyborgs over Gilmore's.