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During Bass's ending in Mega Man 2: The Power Fighters, when Dr. Wily is telling Bass about his powerful new creation, he also tells him about his "other project", possibly hinting at the Maverick Virus.
According to the Rockman Zero Collection Timeline, Dr. Light made X with a perfect virus countermeasure because of an unknown computer virus of alien origin that caused robots to become violent and riotous. This virus is believed to be a precursor of the Maverick Virus or perhaps even the Maverick Virus itself. In addition, trace amounts of the virus were also sealed inside Zero's capsule.
Transfer to Sigma
Around the same year X was discovered, and the Reploids were developed from reverse-engineering X's design specs, trace amounts of the computer virus leaked out to the various Reploid population from within Zero's capsule, thus resulting in the creation of Mavericks, and likewise the formation of the Maverick Hunters. Zero, having somehow escaped from the capsule he was locked inside, fought the Maverick Hunters, destroying several of them. When Gamma Unit was entirely destroyed by Zero in an attempt at sealing him inside the ruins he was found, the leader of the Maverick Hunters, Sigma, decided to intervene by fighting against the red Maverick. 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.
Sigma and Zero ended up being infected by the Maverick Virus due to being in close proximity to Zero's capsule, as well as the damage they both sustained. 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 to be taken to a repair center and be examined by Dr. Cain. The Maverick Virus, however, had a noticeably different effect on Zero. As Zero was built as an absolutely evil robot, the virus had an unexpected effect on him, causing him to become good instead, and he joined the Maverick Hunters. 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 battlefield 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 Doppel Town, it seemed the world was finally safe. Unfortunately, the nightmare returned when Dr. Doppler went Maverick. With Doppel 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 that none other than 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 the crash site, 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 (implied to be Wily), 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, while Zero goes missing for weeks.
During Mega Man X6, Earth is shown to be heavily damaged due to the virus and Eurasia's crash, forcing the humans to take refuge underground while the Reploids attempt to restore the planet. Gate, a scientist and former colleague of Alia, investigates the crashed site 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 reputation. Gate leads eight researchers to "investigate" the problem, but they are actually baiting Reploids to be affected by the Nightmare, 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 also found DNA of Sigma and revived him. Fought in a half-finished body, Sigma is once again destroyed. It was discovered that 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 a defected Syndicate member, Axl. However, Red Alert was being manipulated from 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, 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 and be analyzed by scientists (as well as by his own accord upon Zero realizing this himself), having his cognitive program separated from his body so the two could be researched separately. Years later, a female reploid scientist (Ciel's ancestor) 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 Maverick Wars had been ended by the powers of the Mother Elf by reverting the viral infection of Reploids caused by the Sigma Virus, Dr. Weil, a weapon researcher and DNA revival specialist who had worked at the same laboratory as the unknown female ancestor of Ciel (who had researched Zero's body) in order to find a way to end the war, felt unsatisfied with the result of the solution. Thinking that it wasn't enough to simply cure the Reploids of the virus while they still posed a threat to society due to their free will, he 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 an 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.
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. 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.