Based between the events of the Game Boy Advance titles, Mega Man Battle Network 1 and 2, Lan and the virtual friend Mega Man are out to stop an evil virus, code names 'Zero' from destroying Cyberspace.
Guide Mega Man through each side-scrolling level, hacking into Cyberspace and killing off the elements of the virus. Choose from a range of weapons loaded on battle chips, which can be selected and downloaded once found. Each chip provides a new weapons or defense option for Mega Man.
Boss battles at the end of certain levels, and puzzle elements through-out, add to the adventure, while Mega Man's strengths can be improved upon RPG style during play.