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.