Mega Man X and his trusty partner Zero have a new force to reckon with. Who or what has caused a riot of Mavericks to break out in the experimental utopia known as Doppler Town?

Named after the scientist reploid, Doppler Town was supposed to be a place where humans and reploids could live in harmony. After discovering a virus that was turning reploids to Mavericks, Doppler's anti-virus was a big success. But Doppler itself became infected with the virus and assembled a team to take out the Maverick Hunter Units. The Doppler Effect is about to unfold, with Mega Man X and Zero the only cure for the deadly virus!

Zero, who had returned as an irregular hunter, became the commander of the Zero Special Forces Unit and continued to sweep up irregulars together with X, who was active as the commander of the 17th Elite Unit, and other hunters in the unit.

At the same time, Dr. Doppler, a scientist-type repliloid, conducted research that revealed the fact that the computer virus "Sigma Virus" was the cause of irregularities, developed a special antibody virus, and proposed that it be injected into repliloids. As a result, the number of irregularities decreased. Furthermore, Dr. Doppler declared that he would build "Doppeltown," a peaceful city where humans and replicants could coexist, and he gained the support of both humans and replicants.

A few months later, however, Doppler and his Repliroids, who had been exposed to the antibody virus mentioned above, rebelled. The Irregular Hunters recognized Doppler and the participants in the rebellion as irregulars, and X and Zero were ordered to go into action.