Lan Hikari, the young hero, is invited to attend a local net-battle tournament with his Personal Electronic Trained character, Mega Man. However, during the tournament, Mega Man and Lan discover a plot by an evil corporation who's planning once again to take over the network.

Mega Man Battle Network 3 is an RPG where you must guide Mega Man through various levels, defeating enemies along the way and collecting various chips to upgrade Mega Man's weapons and other items.

This is one of two complementary versions of the game (the other being the Blue/Black version), although initially there was only the White Version when it was first released in Japan. Both versions come with a set of exclusive content, most notably the Giga chips, a new class of chips that can only be used in their respective game, but also including different bosses and a battle style unique to each version. Standard and Mega chips can be traded between the White and Blue/Black versions of Mega Man Battle Network 3.