The player character awakens in a cave with no memory of how he came to be there. He finds a village of Mimiga, who are being persecuted by the Doctor. The Doctor's servants Misery and Balrog are looking for Sue Sakamoto, a girl who had been transformed into a Mimiga. Not finding her, they mistakenly abduct another Mimiga named Toroko instead. The player finds Sue in the Egg Corridor, where she discovers the egg of a Sky Dragon, which could allow her to escape the floating island if hatched. Sue attempts to rescue her brother Kazuma, but King, the leader of Mimiga Village, captures her and holds her responsible for Toroko's kidnapping. Sue tasks the player with retrieving Kazuma from Grasstown. After freeing him, they meet Professor Booster, who reveals that the Doctor plans to use the red flowers on Mimigas to create an army to take over the surface world. Booster sends the player to the Sand Zone to destroy the red flowers before the Doctor can find them. While there, the player meets Curly Brace, a female robot who also has no memories of her past, and Jenka, an old witch who is Misery's mother and guardian of the red flowers. Jenka calls the player character a "soldier from the surface", one of many who were sent to the island to slaughter the Mimiga. Balrog manages to steal the key to the warehouse containing the red flowers from Jenka, who urges the player to stop them. Before the player can reach the warehouse, however, the Doctor force-feeds the captured Toroko a red flower and fatally injures King, leaving the player to fight the rabid Toroko, who ultimately dies.