After the Omega Maverick War, the Maverick Hunters had a new leader, Signas, who was known for the advanced CPU he was built with. He proved to be a good assest to the hunters.

However, a strange event occured. The hunter base was under attack, and by Sigma! Zero was damaged by him, but X was able to destroy the Sigma form.

However, it was discovered that Sigma was releasing a type of Sigma Virus all over the world. This virus, however, didn't cause reploids to go Maverick, but inflicted agreat amount of damage to the infected reploid, except for one, Zero. If Zero would get infected with this new virus, his power would increase, and thus become invincible.

It was also discovered that the abandoned space colony of Eurasia was unstable and was heading towards Earth. The Hunters had to stop the assult, and only two options were open to them, a high powered cannon known as the Enigma Cannon, or to use an old shuttle to run into the colony. However, each item needed to be repaired, and each itme was located in an area were a potential Maverick was located. However, there was only 18 hours before the collision, and each investigation took an hour and the base had periodic attacks by a mercenary reploid known as Dynamo. X was once again aided by Dr. Light, but with two armors instead of one, but to function without interference from the virus, all four pieces had to be collected.

The first attempt, the Enigma Cannon, failed, so that left the shuttle, and it was piloted by Zero. The shuttle was able to destroy the colony, but it didn'tcompletly destroy the colony. The huge chuncks that remianed crashed onto the Earth, cause mass damage world-wide.

The hunters' troubles were just starting. Sigma made his final appearence and X and Zero had to stop his final plan. It was finally discovered what his plans were, to make Zero Maverick, so he could unlock his full power. Sigma was defeated, but only at a high cost, Zero was killed at the end. X could only mourn for a bit before the entire base was destroyed. X emerged to face a new challenge, with Zero's saber in hand.

The humans took refuge underneath the ground while the reploids and some humans remained to begin work on the reconstruction of the Earth. However, three weeks later, strange things began to happen. With the appearence of 'Nightmare Zero', a reploids began to disappear and a reploid known as Issoc was on a quest to turn reploids from the restoration project. X had to lead a few hunters to investigate the 'Nightmare Investigators'. However, it was discovered that the Investegators were actually reploids that were destroyed in the past. The Nightmare Zero proved to be a false replica of Zero, and Zero made a startling reappearence and helped X with the investigation.

The Nightmare was discovered to be a type of high virus aimed at low or inhured Reploids, which made the task of rescuing reploids from the 'Investigator area' a top priority.
With the defeat of the Investigators and the reploid known as 'High Max', the true mastermind behind the Nightmare and the Investigators appeared. The rpeloid was known as Gate, a reploid scientist who was known for his achievements in reploid studies and a former collegee of Alia's.

X and Zero lead an assult on Gate's labratory and faced Gate. It was discovered that Gate had aquired a piece of Zero from after the Eurasia incident and developed the Nightmare and the Investigatores based on Zero's data. Gate also infused himself with the same data, and the only was to damage him was to use his own weapons against him.

Gate was defeated, but it was discovered that Gate tried to recreate Sigma with the new data he had gained, but Sigma destroyed Gate and challenged X and Zero. It was assumed that Isoc was the 'host' for Sigma, which is assumed took place during the 'Eraser' incident.

Sigma hadn't fully been recontructed, and his defeat proved to be easier than expected, and Sigma was defeated with ease.
The reconstruction of Earth could continue, but after a few months, Zero had once again disappeared. X tried to search for him, but the Earth restoration took priority.