Mega Man, Proto Man, and Search Man are sent inside the cyber world of Duo's Comet to avert Earth's destruction. Dark Mega Man enters Duo's Comet at the same time in an attempt to gain Duo's power and become the most powerful navi in the universe.
- Evil Counterpart: Dr. Hikari and Regal both note that Dark Mega Man knows Lan's attack patterns and can counter whatever battle chip Lan uses, making him this to both Mega Man and Lan.
- Eviler than Thou: Dark Mega Man is literally stabbed in the back by Slur for entering Duo's Comet.
- Friendship-Hating Antagonist: Dark Mega Man questions Regal about people desiring bonds. His answer is that people are weak cowards and fear loneliness noting that they can't survive alone and seek companions.
- Killed Off for Real: Dark Mega Man is deleted holding off Slur with a Salamander battle chip long enough for Mega Man, Proto Man, and Search Man to escape.
- The Power of Friendship: Mega Man tells Dark Mega Man that individuals like himself and Lan have limited strength, but by working together, their strength magnifies and that with the strength of bonds, two people can be as powerful as ten or a hundred.
