Mega Man X6

Following the Eurasia space colony incident , which nearly destroyed planet Earth, the Maverick Hunter Zero remains missing in action and presumed dead, with his partner X remaining as the world's best Maverick Hunter. As a result of the space colony's impact, Earth's surface has been rendered largely uninhabitable, forcing the human population to take refuge underground. An intelligent Reploid researcher named Gate, researching the impact site, discovers an unusual piece of wreckage. A week later, Gate loses his sanity as he secretly experiments on the mysterious item and declares his intention to turn Earth into a utopia for high-class Reploids.

Maverick Hunter operator Alia sends X to the crash site to investigate the disturbance. During his mission, he briefly encounters a ghostly being reminiscent of Zero . X then meets a Reploid scientist named Isoc and his nigh-invulnerable subordinate, High Max. They are in search of the Zero-like being, dubbed the Zero Nightmare, which is spreading a dangerous "Nightmare Virus" that causes Reploids to falsely perceive reality to the point of harming themselves and others, turning them into rebellious "Mavericks".

Isoc invites all Reploids to join his cause to destroy the Nightmare Virus and dispatches eight Reploid "Nightmare Investigators" to investigate areas with high Nightmare Virus activity. X follows the Investigators to the suspected areas himself and fights them as they each become infected. After each is defeated, Alia gradually reveals her history as a previous colleague of Gate's; Gate had built the Investigators during their tenure together, but a group of jealous rivals murdered each of them in a series of staged accidents. Optionally, X can also encounter the Zero Nightmare and defeat it.

Following this, the real Zero appears, unaware of how he survived his battle against Sigma. Nonetheless, he reunites with X and rejoins the Maverick Hunters to continue investigating the Nightmare Virus. After this, X and Zero can find and encounter High Max, defeating him in battle. Following the defeat of the eight Investigators or High Max, X and Zero are contacted by Gate.

Gate reveals that the item he found at the crash site was a piece of Zero's DNA. The DNA drove Gate insane, and he used it to create the Zero Nightmare, the Nightmare Virus, and High Max to help build his utopia. The Hunters go to Gate's laboratory to put a stop to his plans. Following Gate's defeat, he confesses he has been rebuilding Sigma , the Maverick who instigated the Eurasia incident.

Isoc loses his consciousness permanently before trying to tell Zero something. Sigma awakens in an incomplete state, incapacitates Gate, and attacks. If X defeats Sigma and previously defeated the Zero Nightmare, Zero is alongside X as he rescues Gate so that Alia can try and revive him if she chooses to do so. If X defeats Sigma but did not defeat the Zero Nightmare, Alia is instead with X at the end and thanks him for rescuing Gate.

Zero is then shown to be alive, but leaves the fighting to X. If Zero defeats Sigma, an unknown scientist seals Zero away for research for the next 102 years, as Zero is worried about the potential of his DNA and believes X can protect the peace in his absence.