The game's story begins in just one of many underground ruins. Our hero, Megaman, is a digger who has just obtained the refractor held within these ruins. Ready to leave, his best friend and spotter, Roll, keeps an eye on her equipment and guides him out over radio. On the way Megaman comes across a huge reaverbot, the boss of these ruins, not about to let the refractor be taken. Megaman battles the reaverbot until it is beaten and shuts down. He makes his way to the surface but Roll, in control of their air ship the Flutter, is nowhere to be seen. As he stands waiting, Megaman suddenly turns to find the large reaverbot has reactivated and followed him to the surface, ready for a rematch. Fortunately Roll shows up just in time to help Megaman make his escape. He hops onto the Flutter's deck and they take off into the sky, leaving the reaverbot and the ruins behind.
While flying through the air Megaman and Roll's conversation is suddenly disrupted by a distressed voice. Roll's grandfather, the famous, now-retired digger Barrel Casket, informs them that the ship is having engine trouble. It soon it becomes evident they will crash if they don't hurry and land somewhere to make immediate repairs.
Roll steers the Flutter toward the nearest island, a place called Kattelox. As they crash land, the Flutter's rudder busts off, and the entire air ship goes skidding across the land some distance before it finally grinds to a halt.
The Casket family, including Megaman's mechanical monkey Data, all make it safely but find themselves stuck on Kattelox until they can make repairs. The local police drive out to make sure everyone is okay, and to welcome them to the island. Soon after, there comes a report that air pirates are heading to the island to steal the legendary treasure supposedly buried there.
So begins the adventure...