Mega Man has been respected as a hero. Then one day,Mothraya,that was created by Doctor Cossack,attack the city. Mega Man gets overpowered,but was saved by Blue. Doctor Light reveals to Mega Man that Blue was created before him & Roll. When his energy core went wrong,Blue walked out. A commotion goes on with 8 Robot Masters. Light sent Mega Man & Roll each mission & gave him a robot dog,Rush.
Roll takes on Toad Man & Ring Man while Mega Man takes on Dive Man & Drill Man. Later,Cossack meets with Doctor Wily,who has kidnapped his daughter,Kalinka & he will release her as exchange for destroying Mega Man. While Roll takes down Dust Man,Mega Man gets overpowered by Skull Man,who somehow gets pummeled by Blue,who is now Proto Man. He reveals that he has been eavesdropping from Cossack's conversation with Wily.
Mega Man goes to Wily's Lair to save Kalinka,but was confronted by Bright Man. Proto Man fights with Pharaoh Man & kills him. Mega Man quickly kills Bright Man & leaves with Kalinka. Cossack sees Kalinka safe. Then,Wily appeared,piloting a giant Robot,Gamma. Proto Man & Roll gets overpowered, But Mega Man tries to intervene. Rush came to his aid & fuse together to become Power Mega Man. He destroys Gamma & Wily disappears through the smoke as he falls.
Before leaving with Cossack,Kalinka thanked Mega Man & hugs him. Light sees Proto Man,who gave him a thumbs up before leaving.