Doppler was a Reploid and an excellent researcher. He watched the war between the Maverick Hunters and Sigma, and hoped he could do something to stop this war. He created the utopian Doppler City, where all Reploids who were tired of the Maverick Wars gathered, with Dr. Doppler as their ruler. He studied the Sigma Virus, and successfully developed a anti-virus vaccine that he soon distributed among the denizens of his city. However, the anti-virus was a fake, and the Reploids start to go maverick in the city.
Doppler gathers an army of Mavericks and starts a full-scale attack against the Maverick Hunters base. X and Zero rush to the base to intercept the attack. X enters the base and finds Mac, who was a Maverick Hunter. He traps X and capture him, telling that he now worked for Doppler. Zero destroys Mac and rescue X, so the both of them goes to Doppler City to find Dr. Doppler and stop him. Doppler hires two police Reploids, Bit and Byte, and also revives Vile to hold off X and Zero.
X defeats Doppler's Mavericks and proceeds to his lab along with Zero. After defeating the fused Bit and Byte, as well as Vile, X finds Doppler and fights him. As X defeats the doctor, he recover his consciousness, revealing that he was being used by Sigma all along, having built a new and more powerful body for him.
X then goes after Sigma and defeats him. When the viral form of Sigma tries to possess X, Doppler intervene by trapping Sigma within his own body, which contained the true anti-virus that he developed. X manages to escape while the lab explodes, as Sigma's code starts to vanish due to the anti-virus effects.
In Battle he shoots Green Orbs, and he generates a force field. The green Force Field absorbs any shots, and converts it into Health. You cannot get this weapon though.
- As with Mega Man X4, fans like to debate which of the two endings is the canon one, since there is no solid indication in the series. While Dr. Doppler hasn't made an appearance in subsequent games, his anti-virus technology seems to live on, most notably in Mega Man X5.
- It is worth mentioning that if Zero uses the anti virus on Sigma, he says that he will come back. However, if Doppler is the one who destroys Sigma, he does not say so. This may hint that the canonical ending is the one where Zero destroys Sigma.
- Dr. Doppler's name is a reference to the Doppler Effect and a pun on Doppler Radar.