During Bass's ending in Mega Man 2: The Power Fighters, when Dr. Wily is telling Bass about his new powerful 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 counter-measure 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 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 against the Maverick Hunters, destroying several of them. When Gamma's 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 which contained the virus inside, 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 Dopple 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, 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 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 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 an AWOL Syndicate member, Axl. Red Alert was however been 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 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.