Zero's Fate After the Mega Man X Series

At some unknown point, Zero realized that he carried the virus inside him and may even be continuing to 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. At the same time, a project was started to analyze Zero as it had been revealed previously (during the Eurasia crisis to be exact), that Zero actually reacted positively to the Sigma Virus, and 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 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 also worked in the lab, planned a different way of dealing with the Mavericks, as he was unsatisfied with the result. Weil started a 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".

Thinking that it wasn't enough to simply cure the Reploids from the virus while they still posed a threat to society due to their free will, Weil decided to create his own, radical solution, while making himself ruler of the world in the process. Project Elpis was the end result: to create a Reploid who would become the perfect ruler, by using the power of the Mother Elf to control all the Reploids in the world, thus preventing them becoming Mavericks in the first place.

However, since the world was at peace at the moment thanks to the Mother Elf, he needed to give the government a reason to sanction Project Elpis. He secretly stole the Mother Elf and reprogrammed her into the Dark Elf, whose purpose was to create Maverick outbreaks by brainwashing Reploids. Baby Elves, small copies of the Dark Elf, were mass-produced to cause violent Maverick outbreaks worldwide.

As new Mavericks arose and caused terror and destruction in scales never seen before, the government heeded Dr. Weil's pleas and sanctioned Project Elpis to bring this new and devastating conflict to an end. For the project he was given Zero's body, which possessed the necessary virus countermeasures for creating the perfect ruler, Omega, the messiah of Dr. Weil.

For Omega to control all Reploids worldwide with the Mother Elf, a massive armor was constructed around Omega for the Mother Elf to fuse with it. In addition the armor also boosted Zero's body to its absolute limits and granted it the ability to regenerate any damage. Along with the armor, Omega received new weapons, suitable for his new size and weight. Unknown to everyone Omega received a new personality, which was absolutely loyal to Dr. Weil's orders. With Omega completed by fusing it with the Dark Elf, the baby elves would be redundant as they were no longer needed.

In the fourth (and what would be the last) year of the war, Zero, in possession of a new body Ciel's ancestor created for him, would wake up so he could fight alongside X against the new threat. At some point during the conflict, which were now known as the Elf Wars, Zero reclaimed the Dark Elf from the mavericks and used her to bring the uprisings to a end.

It was then where Weil revealed his true colors and ordered Omega and a group of Mechaniloids, similar to Neo Arcadia's later Golem models, to attack his former allies. However, because Zero reclaimed the Dark Elf in time, Omega was unable to fuse with the Dark Elf. He was defeated after a hard battle by X and Zero using the Final Strike.
After the war had ended, Zero decided to seal himself away again, this time, forever. Though X tried desperately to stop his friend, the sealing process had already begun when X arrived, and could not be stopped. Before he lost consciousness, 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 human kind, just as X believed in them. With these final words, Zero's seal was complete.