Lan Hikari and his friends, Dex, Mayl and Yai, are called to the SciLab headquarters for the announcement of the latest research project that Lan's father, Yuichiro, has been working on. Before he can reveal it to them, mysterious agents take over SciLab, subduing everyone with sleeping gas, kidnapping Yuichiro, and stealing their PETs (a device that contains the program avatars called NetNavis). However, Lan was in a different section of the lab and avoids being discovered or having his PET stolen. The agents turn out to be working for Dr. Regal and his crime syndicate Nebula, which has returned after being defeated in "Mega Man Battle Network 4". Nebula subsequently takes over the Net with an army of viruses and Darkloids: NetNavis that use dark powers and Dark Chips.