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Transfer to Sigma
Before the events of Mega Man X, Zero, who at the time was a Maverick, fought against the Maverick Hunters, destroying several of them. The majority of the destruction he caused, however, was with the Maverick Virus he unknowingly carried within him, causing the few reploids to get near him and survive to go berserk. When the entire Gamma Unit was destroyed by Zero, the leader of the Maverick Hunters, Sigma, decided to intervene by fighting against the red Maverick in an old abandoned laboratory. Even Sigma, the most advanced and powerful of the Maverick Hunters, sustained heavy damage. After a grueling battle, Zero had beaten Sigma into submission, and was attempting to pull off the commander's head; however, before he could, a W appeared on Zero's helmet crystal and caused him to cringe in pain. Sigma punched this crystal, shattering it and defeating Zero and, subsequently, passing on the Maverick Virus to himself. As Sigma was too strong to be infected by the Maverick Virus, the virus instead adapted to him, creating the Sigma Virus. Sensing something strange, Sigma ordered Zero taken to a labratory to be examined, where he would later awake with a completely blank mind. However, he still carried a small part of the original virus in himself. Meanwhile, the Sigma virus was transmitted throughout the Maverick Hunters, leading to the betrayal of Sigma and several other high-ranking hunters.
As the Sigma Virus
Within Sigma, the virus grew and evolved. Though created by Dr. Cain as the most advanced Reploid with technology that kept him from going Maverick, the virus was a catalyst unlike any seen. Eventually, Sigma started a rebellion against humans in the game Mega Man X, and recruited several Maverick Hunters into his army, both voluntary and forcibly. Though he had no knowledge of the virus yet, this was a foreshadowing of an ongoing war between Reploids and Mavericks known as the Maverick Wars.
After Sigma's defeat in the first game, X had thought the Maverick problem and Sigma's rebellion was over. However, six months later, this turns out to be far from true, and X is called out into the battle field again. After battling through hordes of Mavericks, the enigmatic X-Hunters, and even a copy of Zero, a revived Sigma reveals himself, only to be destroyed one more time. It is revealed Sigma's program merged with the virus, and he became a virus known as the Sigma Virus.
In Mega Man X3, a brilliant Reploid scientist named Dr. Doppler creates a Neuro Computer, which finally neutralized the Maverick problem. Living peacefully in a gathering dubbed Doppler Town under Doppler's watch, it seemed the world was finally safe. Unfortunately, the nightmare returned when Dr. Doppler went Maverick. With Doppler Town's inhabitants on a rampage, X and Zero are called to destroy the Mavericks and bring Dr. Doppler to justice. After destroying the eight Mavericks leading the revolt, they find none other then Sigma was behind Dr. Doppler's actions and ordered him to build a strong body for him. After destroying Sigma yet again, the Sigma Virus reveals itself. With the power to bend Reploids to his will, it attempted to take X's body and use it as his own. Sigma corners X, only to be saved in the nick of time by Zero (or Dr. Doppler, depending on how the game is played), who uses a cure for the virus created by Dr. Doppler, apparently destroying Sigma.
Later, during the events of Mega Man X4, Sigma returns, planning on using a satellite weapon to attack humankind. This time the virus is unseen, though, but its origins are mentioned in a flashback.
During the events of Mega Man X5, Sigma purposely loses a battle against X and Zero, spreading the Sigma Virus over a large area of the planet. Meanwhile, a mercenary named Dynamo was hired by Sigma to scatter a virus in the space colony Eurasia and prepare it to crash into the Earth. Seeing no other choice, the Maverick Hunters prepare the Enigma cannon to destroy the colony. If the Enigma fails, Zero pilots a space shuttle to crash into Eurasia. Alia, a navigator new to the Maverick Hunters, reads a signature like the Sigma Virus, but with differences. This Virus is dubbed the "Zero Virus". Fighting through multiple enemies in Eurasia's crash site, X and Zero battle each other, coming to a draw, and Sigma appears before them. Retreating further into his base, Sigma reveals that his plan for Eurasia's crash was to actually awaken the "true Zero", using a large amount of the Sigma Virus and merge it with the Colony Virus (a variety scattered on Eurasia) to infect Zero. Sigma tells them of an old man he met, who has an undying hatred for X and knows all about Zero. Sigma is fought, and despite his defeat, manages to obliterate both X and Zero. X is repaired by Dr. Light, somehow able to appear through a mysterious force, and Zero goes missing for weeks.
During Mega Man X6, the virus is running full force after it was scattered, forcing the humans to take refuge underground while the Reploids attempt to stop the situation. Gate, a scientist and former colleague of Alia, investigates the crashed sight of Eurasia. Finding a strange piece of Zero, a new set of Maverick outbreaks occur, and X is called out once again. In the heat of battle, a strange purple version of Zero helps him. Now called the Zero Nightmare, this being is believed to be behind the new Nightmare Virus that is infecting Reploids, destroying Zero's legendary reputation. Gate leads eight researchers to "investigate" the problem, but they are actually working for him and X goes and destroys them. The Nightmare is defeated, and the real Zero returns. Gate, angry at X's actions, directly challenges him and allows him to enter his lab. When Gate is defeated, he reveals that he not only found DNA of Zero and used it to create High Max and the Zero Nightmare, but he is also found DNA of Sigma and revived him. Fought in a half-finished body, Sigma is once again destroyed. It was discovered Zero is the source of the virus, and he scattered it around the world during his missions as a Maverick Hunter.
During Mega Man X7, the virus mostly disappears from Earth, and the chaos after Eurasia's incident was reduced greatly. Next Generation Reploids are now in production, and the Red Alert Syndicate challenges the Maverick Hunters for the custody of an AWOL Syndicate member, Axl. Red Alert was however manipulated behind the shadows by Sigma, who reprogrammed most of the Red Alert generals. The virus was still very weak after the events of Mega Man X5 though, but at least one member of Red Alert was apparently infected by it.
In Mega Man X8, Sigma attempts to defeat X, Zero and the now full-time Hunter Axl. In the battle, Sigma is believed to be destroyed once and for all. However, the director of the Jakob Project, Lumine, steps from the shadows, and reveals that, having a copy of Sigma's program inside their copy chips, all New Generation Reploids can go Maverick at will.
After the Mega Man X series
After discovering Zero was the source of the virus, he was ordered to be sealed to be analyzed by scientists, having his cognitive program separated from his body so the two could be researched separately. Some years later, a Reploid scientist (Ciel's great-grandmother) discovered an antibody to the Sigma Virus in Zero's cognitive program. She used it to create the Mother Elf, a lifeform able to rewrite and erase the Sigma Virus. Afterwards, the scientists researching the virus focused on creating Cyber-elves to eradicate the virus. X used the Mother Elf to end the Maverick wars, dropping the number of Mavericks significantly.
After the war, a member of the humans researching the Cyber-elves proposes Project Elpizo (Project Elpis), an operation to create a Reploid that could control other Reploids using Mother Elf's abilities, being a perfect ruler. X opposed the project, but fearing a long-lasting war, humans support it. They debate if humans should coexist with Reploids or control them.
Dr. Weil stole Zero's body and used it to create Omega, and he transformed the Mother Elf into the Dark Elf, beginning the Elf Wars. X and Zero (using a copy of his body) manage to defeat Omega with the Final Strike, putting an end to the war. Nearly 90% of the Reploids and 60% of the humans were lost during this war.
After this, Dr. Weil was banished from Neo Arcadia, and Omega was ejected into space. Zero returns to his slumber and X became the main ruler of Neo Arcadia. Some time after, in order to stop the Dark Elf from causing more harm, X uses his body to seal her in Yggdrasil. However, because of this, X's absence caused problems for Neo Arcadia and Ciel was commissioned into building a replica of X. The Copy X, leads the rest of the armies from here and destroys any remaining Mavericks left after the war. By this time, the Sigma Virus was no longer mentioned, believed to have been finally put to rest once and for all.