At some unknown point after his mission on Gigantis, Zero realized that he carried the virus inside him and spread it all over the world during his missions as a Hunter. Thinking that the world wouldn't be safe as long as he was still active, Zero admitted himself into a research institute, in order to get rid of the virus within him that caused Reploids around him to go Maverick. At the same point, a project was started to analyze Zero as it had been revealed previously (during the Eurasia crisis to be exact), that Zero actually reacted positive to the Sigma Virus, therefore might hold anti-bodies for the infection. Zero was sealed away and brought to a government lab. At some point, Zero's mind was extracted from the body, possibly for security measures in case something would go wrong while researching it.

For an unknown amount of time, Zero's body was studied by government researchers. One of them, an unnamed female ancestor of Miss Ciel, managed to create the "Sigma Antibody Program", a Cyber-elf capable of reverting the devastated programming of infected Mavericks and therefore destroying the virus completely. This Cyber Elf was the Mother Elf.

However, weapon researcher and DNA revival specialist Dr. Weil, who worked in the lab as well, planned a different way of dealing with the Mavericks, and was unsatisfied with the result. Stealing Zero's mindless body and the Mother Elf, Weil started a horrible conflict that would ultimately cost the lives of 90% of all Reploids and 60% of all humans. This four-year-long period of war was later dubbed the "Elf Wars".

Weil, who used the Mother Elf (now known as the Dark Elf) and copies of her, known as Baby Elves to gain control over Reploids all over the planet, ordering them to destroy each other, worked on Zero's body, manufacturing an exterior armor around him which boosted the body's specs to its limits as well as granting him the ability to control all Reploids at the same time when combined with the Dark Elf and creating a new consciousness for the body loyal to him: Omega.

When the Elf Wars were in their fourth and final year, Zero reappeared on the battlefield, given a copy of his old body (however, it is still unknown who created the body, but it is presumed it was Ciel's ancestor). Zero managed to infiltrate Weil's laboratory and steal the Dark Elf from Weil. He then ordered every Reploid in the Dark Elf's range to turn against Weil. At that point, Omega was released onto the battlefield, along with a few Mechaniloids, to defeat X and Zero and retrieve the Dark Elf. Zero, who by that time had realized Omega was using his original body, defeated him together with X by using the Final Strike, disabling the massive Reploid.

After the war had ended, Zero decided to seal himself away again, this time, forever. Though X tried desperately to stop his friend from sealing himself another time, the sealing process had been gone too far to stop it. Zero told X that, as long as he was still around, the bloody history would repeat itself over and over again. Before the seal was complete, he encouraged X that this was the right way and that he wanted to believe in the humans as X believed in them. With these final words, Zero's seal was complete. However, the seal is not eternal, and, a hundred years later, he will awaken to face more battles.