Mega Man X6 takes place 3 weeks after a space colony called Eurasia crashed into Earth, making the planet uninhabitable for humans. The survivors live underground, while Reploids try to recover from the Sigma Virus attack.
The Maverick Hunters, led by X, face a difficult task in their quest to help with the recovery operation. With his partner Zero lost in the attack, X is left with only his Beam Sabre as a reminder of what he's lost. A young scientist named Gate discovers a mysterious chip and sends 8 assistants on a mission to find answers about the "Nightmare Virus". However, when they vanish, it's feared that they've turned Maverick.
X is now the only one who can uncover the truth behind the "Nightmare Virus" and perhaps understand Gate's motives. With this new challenge, the sixth episode of Mega Man X begins.