In the world of Terra, the planet is covered in water. Islands are the only land left. Under the land is an ancient civilization filled with powerful robots called Reaver Bots. The world above and below are connected the Sub Gates, buildings containing a ladder or elavator. To power things, people need Quantum Refractors. The only place to get a refractor is in the ancient civilization. Diggers go in to the the ancient civilization to get refractors. It is dangerous, but they must do it to keep their world from being like the world below. Air Pirates, though, take Diggers' refractors to sell them for their own profit.

MegaMan, his sister Roll, their monkey Data, and their grandfather, Barrel, are a family of diggers. They crash lands on Kattelox island, and they can't leave until their airship is repaired. But before that happens, they discover the island's greatest secret.

This was the first 3D MegaMan game. A lot of people said that it wouldn't work, but they have been proven wrong. There have been a couple of spin-offs and cameos of this game, but there has been only one true sequel which is MegaMan Legends 2. People are awaiting the second true sequel in this great series.