The game is set in the Battle Network setting (specifically the first Battle Network title), but both MegaMan.EXE and Geo Stelar (as Mega Man) appear together and are playable. The game is largely identical to the original title with the exception of an extra chapter involving Geo's appearance and a battle against a new NetNavi named ClockMan. However this chapter is completely disconnected from the storyline of the game and is not mentioned again afterward. In the prologue, Harp Note is kidnapped by ClockMan.EXE (a NetNavi able to travel through time by creating warp holes), who escapes to the Mega Man Battle Network era 200 years in the past. Dr. Goodall prepares a warp hole to allow the Star Force Mega Man to follow them, and warns him that he can only return to his time if he finds ClockMan.