Thirty years ago, Duo's comet had crashed on Earth, and Dr. Regal plans to travel through space and time to absorb its power. MegaMan, ProtoMan, SearchMan, and Colonel rush through time to thwart Dark MegaMan who was sent to help Dr. Regal gain access to the comet. However, Dark MegaMan plans to absorb the power himself and become the ultimate NetNavi, but Slur refuses to allow him to do so by deleting him. Before fading away, Dark MegaMan self-destructs and prevents Dr. Regal from succeeding. The heroes return home, and the renmants of Dark MegaMan's being rejoin with MegaMan's soul, and MegaMan forgives him.