Mega Man Legends 2 begins shortly after the story of Mega Man Legends ends. Far in the future when most of the continents on the earth have sunk into the sea, a unique civilization is formed on a small patch of land that remains. The people's lives are sustained by explorers called "diggers" who dig ancient ruins to collect energy sources called Refractors, a substance this world can not live without. In Mega Man Legends 2, Mega Man and friend Roll, are Refractor diggers. They travel the world in search of the "Great Legacy," a dream many diggers share, but nobody really knows much about. Verner Von Bluecher, an entrepreneur, preaches the theory most widely believed: that this new energy with will provide infinite power and will eventually replace Refractor. It is Von Bluecher's wish to travel to the "Forbidden Place" in a huge airship where it is rumored the Great Legacy exists. As he starts to set sail, a mysterious woman appears and the adventure in Mega Man Legends 2 begins.
