The premise of the compilation involves the evil Dr. Wily building himself a time machine to travel back in time in an attempt to defeat the robotic hero Mega Man in one of their first three conflicts. In order to stop Dr. Wily, Mega Man was sent into the past in a time machine hastily crafted by Dr. Light, where he relives his earlier adventures in which Wily dispatches a set of powerful robots to take over the world which must be single-handedly stopped as before. After completing his travels through time, Mega Man must use all that he's learned and tackle the Wily Tower.