The NetSavers are in investigation with the Sci-Lab over the strange comet that has appeared in Earth's atmosphere. Soon, strange activity begins occurring when giant-sized Mettaur viruses begin terrorizing DenTech City. Lan and Chaud manage to defeat them, but MegaMan finds himself captured by none-other-than Bass. He tells MegaMan that he is after his "Ultimate Program" so he can fight off Duo. As Lan and Chaud rush to his rescue, they encounter an old rival, Dr. Wily, who seems to know what's going on.