The Maverick Wars (イレギュラー戦争 Iregyurā Sensou?) are a series of global conflicts between the forces of Mavericks, led by Sigma, and the Maverick Hunters and their allies, led by X and Zero. The war begin as the The Day of Σ occurred. The subsequent rise of Mavericks as global enemies, as well as the formation of Maverick Hunters were the primary catalysts of the conflicts. Only Reploids were used in the wars, hence the name.
They began in the year 21XX, when Maverick Zero released the Maverick Virus into the Reploid population, causing some to become destructive and turn against everyone, including their human masters. Later, the virus infected Sigma, current leader of the Hunters, where it, in the process of adapting to his advanced circuit designs, transformed into the Sigma Virus, which contained Sigma's own spirit and aims. Due to this, the Maverick Wars continued for a long time, as the Sigma Virus proved incredibly resilient to deletion and waged war as long as it existed.
Dr. Thomas Light created a robot he named Mega Man X. X is the successor of the original Mega Man, and he was the first of its kind to be able to think and make its own decisions. Fearing that this new robot could be dangerous, but lacking the time to find out for sure himself, Dr. Light sealed X in a capsule to be opened in the future when the robot’s loyalty could be determined.
A man by the name of Dr. Cain found X’s capsule and released the robot despite the warnings Dr. Light had posted on the capsule. This new scientist was immediately impressed by X’s advanced, human-like intelligence. Using X as a model, though there were things he had to change since he either didn't understand how they worked or he wasn't able to duplicate them, Cain created more robots similar to X which would be known as Reploids. Unfortunately for Dr. Cain, Dr. Light’s greatest fear came true. The new robots rebelled against humankind and became powerful enemies known as Mavericks.
Because of this, Dr. Cain is asked by the council to put a stop to this. He forms a special unit to stop these Mavericks known as the Maverick Hunters. However, the leader of the Hunters and Dr. Cain's creation, Sigma, goes Maverick himself, taking many of the Hunters with him. Thus, the "Maverick Wars" begins to take shape...
True and loyal, X took it upon himself to stop the Mavericks and Sigma. X wasn't alone, however. He was almost immediately aided by the mysterious Zero. He also encountered capsules left by the late Dr. Light, which possessed holographic messages and useful power-up items from the scientist. Using these power-ups, X increased his meager abilities and brought himself back on par—and beyond—with his enemies.
During a climatic fight with Vile, Zero sacrificed himself to save X, allowing X to slay Vile. Alone now, X went on to defeat Sigma and bring the Maverick uprising to a halt.
Eventually more Reploids went Maverick, spawning a group of sane robots to reform the Maverick Hunters. Led by X, they struggled to fight off the forces that were trying to eliminate all of mankind. During this, X discovered that Zero’s parts were in the hands of three X-Hunters: Agile, Violen, and Serges. X also discovered exactly into whose hands Zero was to be delivered - namely, Sigma.
Despite the odds, Zero was rebuilt, no worse for wear, and the Maverick Hunters put Sigma out of commission.
For a time.
This is where the tale of Mega Man X2 ends and the story of Mega Man X3 picks up. Dr. Doppler, a Reploid scientist, is possessed by a virus that is none other than Sigma himself, reduced to portable computer code. Sigma finds bounty in this form, however, since it allows him to inhabit whatever robot body he wants. He gets Doppler to construct for him a giant, invincible body, but almost before he can get inside it, X shows up at his front door to take him down.
Sigma’s third fall to a special anti-virus developed by Doppler is no more guaranteed to be his last than any of his others. In fact, he pops up perfectly healthy in Mega Man X4 to start a war between the Maverick Hunters and the elite fighting team known as the Repliforce. He does it again in Mega Man X5 to cause a cataclysm related to the space colony Eurasia which crashes into the Earth. The Nightmare Phenomena in Mega Man X6 which plagued Reploids and created some unusual circumstances were in part a result of Sigma's doing. Sigma was also behind the attacks by a Reploid group called Red Alert in Mega Man X7, where Axl’s shape-changing abilities were the prize. Sigma even had his gloves in the events of Mega Man X8, although it isn't clear whether or not he is the one entirely to blame. It is yet to be seen what, if anything, will be required to finish Sigma off for good.
On the other hand, the Maverick Hunters, by now in full swing with X and Zero being the key players, are joined by Signas, Alia, and others helping behind the scenes, as well as the Reploid known as Axl who has become a full-fledged Hunter. Axl is a prototype to a new generation of Reploids which can copy the appearances and abilities of other Reploids. By the time of Mega Man X8, such Reploids are being mass-produced. This can only result in chaos, and what humans remain are now attempting to flee to the moon, abandoning the earth to the mayhem that their Reploid creations caused.