Legions of highly destructive Viruses have infiltrated NetCity and blocked its main link from the human world. Worst of these are the terrible Cloudy Viruses, which have unleashed a destructive rain on the city that threatens to wash away all its data, jeopardizing everything in the world that depends on it. Taking refuge beneath the streets after narrowly escaping the virus pack, MegaMan, Roll, and Glide encounter TorchMan, who has been badly wounded by the powerful and evil FreezeMan. From TorchMan they learn of a factory where these viruses are produced. MegaMan, Roll, and Glide set out to find the virus factory and destroy it while TorchMan remains behind to meet his fate.