|Location||Dr. Wily's Lab|
|Nano Item||IQ sample|
|Voiced by||Ian James Corlett|
|“||Hey, Roll! I think Dr. Wily is planning something!||”|
Mega Man is Roll's older brother and Dr Ligt's robot son. Dr. Light's lab was destroyed by Fusions, so Dr. Light and Dr. Wily decided to work together. Nevertheless, Mega Man and Roll don't trust Dr. Wily as Dr. Light does. Even though Mega Man doesn't trust Wily, he will not join Roll in attacking him. When Mega Man wants to get away from Dr. Wily, he goes out and plays fetch with Rush and trains with Dr. Wily's robots.
In Mega Man's Nano mission "Doctors Are The Worst," Doctor Wily is found to be missing. He has apparently teamed up with Dr. Eggman, both of them planning to launch an attack on the entire Earth. Mega Man asks the player to help him infiltrate Eggman's new Death Egg. Once they do, they defeat the Egg Dragoon, which has Wily and Eggman inside. Afterwards, in a long battle, the player defeats the mad doctor duo.
Wily apologizes, and returns to working with Light. Dr Eggman had escaped, and is in the West City Sewage Plant. It is completely controlled by Dr Eggman, and is a level 30 area. There are no fusions there, except one. The Fusion is Fusion Mega Man (SF), and has a secret lair that is undetected. Mega Man and the player then go into a room for further investigation, where they see four Fusions trying to steal data. The player retrieves the data, and two black-hooded Fusions manage to escape. The other two have the Master Emerald, all seven Chaos Emeralds, and the data on DexLabs.The player defeats Fusion Mega Man and Fusion Kid Goku, which helps players to get Mega Man's Nano.
Dr. Eggman was revealed to be alive and the dead one was a decoy. Eggman escaped the Death Egg, and Sonic is furious that Eggman faked it all.