The Cyborg 009 team manages to reactivate Leonid's cyborg body, and he begins to regain his memories. However, his experiences as a captive and the trauma he endured have left him shaken. As he struggles to come to terms with his past and his new existence, the team helps him to recover and readjust to his life as a cyborg.

Black Ghost had been experimenting on Leonid, attempting to replicate the success of the cyborg project. However, their efforts resulted in a catastrophic failure, and Leonid's body was severely damaged. In a desperate bid to save his life, the scientists at Black Ghost merged Leonid's consciousness with an advanced AI system, erasing his memories and reprogramming him to serve as a sleeper agent.

The Cyborg 009 team returns to their secret headquarters and begins to analyze the data they recovered from the abandoned laboratory. They uncover a hidden log entry from Dr. Gilmore, the creator of the cyborg project, which reveals a shocking truth: the original cyborgs were not just random individuals chosen for the project, but were, in fact, selected based on their latent potential to become something more.

In a daring move, Joe and the team manage to defeat the Black Ghost agents and escape with Leonid. However, they soon realize that the Rebirth Project cyborg is now on the loose, threatening to wreak havoc on the world.