It's been 3 weeks since the space colony "Eurasia" crashed into the Earth. Since then, the Earth has become a deadly, barren wasteland, unfit for humans to inhabit the surface. The humans now live underground, while Reploids begin the task of attempting to recover from the deadly onslaught of the Sigma Virus.
For the Maverick Hunters, the task is difficult, especially for X. Zero was lost in the attack, and all X has left of him is his Beam Sabre. As the Maverick Hunters assist in the recovery operation, a young Reploid scientist, Gate, discovers a mysterious chip in the wastelands. He immediately sets out on a cause to discover the mysterious "Nightmare Virus", and sends 8 assistants out to search for answers. But when Gate's assistants suddenly vanish, the worst is feared: they've gone Maverick.
X is the only one now who can discover the answers needed to unravel the mystery of this deadly "Nightmare Virus", and perhaps find out what it is exactly Gate wants with it.