After suffering an unknown injury and being presumed dead by his girlfriend, Michi, Naku was rebuilt as Cyborg X by Omega. Omega later sent X to deliver a TV Screen to Dr. Gilmore so he could issue a challenge to him. As he was heading back, X noticed Michi preparing a memorial for him and went to talk to her. He later encountered 009 and 003 and abducted the latter, taking her back to Omega's island base.
When he visited her in her cell, 003 brought up how X had fixed a rose archway after tipping it over, prompting X to think of Michi. However, Omega quickly shocked him for thinking "incorrect" thoughts.
X later bumped into Cyborg 007 who bragged that 009 was going to defeat him and that even Michi wanted him to win. X responded by taking 007 prisoner, and later declared that defeating 009 was no longer his order, it was his will.
During his fight with 009, X accidentally fatally wounded Michi. Abandoning his mission, X freed 003 and 007 before grabbing both Michi and the Cobalt Bomb and flying back over to Omega's base. X rammed his ship into the island fortress, causing the Cobalt Bomb to detonate and kill both him and Omega.