It's been many years after Sigma's last appearance, and things have been going relatively peacefully for the Maverick Hunters. Aside from the occational Maverick out-break, things are going good. Needless to say, Sigma decides to crash in on the party. X and Zero are rushed into action to stop him as quickly as possible.
X and Zero manage to stop the maniac, but in the process they release the deadly Sigma Virus on the earth (completing Sigma's new plain). The Sigma Virus is the program that causes the Reploids to go Maverick. Also, the space station, Eurasia, has sustained severe damage from the battle with Sigma and his on a collision course with earth. X and Zero have 16 hours to stop the station. Lets go maverick hunters!