After the events of Megaman Battle Network and Megaman Network Transmission, life returned to its usual course for Lan Hikari and his comrades. But the summer holidays have barely started when cybercrimes start up again. Indeed, in the absence of the WWW, a new criminal organization, Gospel, has taken over. Lan and Megaman.EXE must therefore return to service and swell the ranks of the Netbattlers (Internet fighters) to prevent the Netmafia from taking control of the Net.