Lan Hikari's standard level NetNavi receives an upgrade, transforming him into the powerful MegaMan.EXE. Meanwhile, TorchMan-a NetNavi working for the World Three net-crime syndicate-has trapped Maylu in a dangerous oven fire.
Mr. Higsby is a rare Battle Chip collector who uses his NetNavi NumberMan to steal chips. He traps Yai and her friends in a classroom, threatening to delete Glide if Yai doesn't hand over her rare chips. Lan and MegaMan, who were locked out of the room, work with Roll to crack passwords and rescue their friends.