Here you can read the whole plot of the game!
The player 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 Kazuma, 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 in the Sand Zone, 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.
Misery banishes the player to the Labyrinth deep inside the island as punishment for interfering with the Doctor's plans. Curly Brace has also been thrown into the Labyrinth and the two cooperate to escape. Balrog helps them to move the boulder blocking the exit, revealing his kind nature. The pair find and defeat the Core, a magical creature whose power keeps the island afloat, but the Doctor steps in to save it before the island collapses. Depending on certain conditions, the player may rescue Curly Brace, who had sacrificed her air tank to save the player character. When the player returns to Mimiga Village, they find that the Doctor has captured the Mimiga.
In the now-ruined Egg Corridor, Kazuma offers the player a choice to escape the island with him using a Sky Dragon, leading to an alternate ending in which the Doctor conquers the surface world while Kazuma and the player hide in the mountains. The player may instead choose to confront the Doctor and destroy the island's Core, which would return the Mimiga to normal.
The player scales the outer wall of the island to reach the Plantation where the Doctor is using the Mimigas as slave laborers to grow red flowers. The Doctor's servants capture the player and place him in a jail cell with Sue. She is taken away before the player wakes up, but her letter reveals that the Doctor was a member of the research expedition that included Sue's family and Professor Booster, but he betrayed them once he found the Demon Crown. Sue directs the player to find her mother who may have a plan to stop the Doctor. If the player saved Curly Brace earlier, they may find an item to restore her memories. Curly remembers that the player character's name is Quote, and that they were not the killer robots who slaughtered Mimigas in the past. Instead, they were sent to destroy the Demon Crown to prevent its power from falling into the wrong hands.
Quote finds Sue's mother, Momorin, who is building a rocket that will allow access to the top of the island where the Doctor resides. After helping her complete the rocket, Quote confronts Misery and the Doctor. The Doctor has purified the essence of the red flowers into a crystal, which allows him to survive even after Quote kills him. The Doctor's spirit possesses the Core of the island, but Quote succeeds in destroying that as well, causing the island to begin falling to Earth. Unless Quote has saved Curly, restored her memories, and acquired the Booster v2.0 from Professor Booster, Sue will lead Quote to jump off the island. The two are rescued by Kazuma and his Sky Dragon, while Momorin, her assistant Itoh, and the captured Mimiga escape on a helicopter, leaving the rest of the island's inhabitants to their fates.
Should Quote complete the aforementioned tasks, they may proceed into the Blood-Stained Sanctuary, a bonus stage where Curly can be found and rescued; it is also here where Ballos — creator of the Demon Crown and Jenka's younger brother — is imprisoned. A powerful wizard who went insane and destroyed his homeland after being tortured by a jealous king, Ballos was sealed deep within the island by his sister. At some point, his niece Misery forced him to create the Demon Crown, but she and Balrog became cursed to serve whoever possessed it. Additionally, it is stated via narration that the Demon Crown will repair itself upon being destroyed, and it will only truly lose its power if Ballos is killed, necessitating that Quote and Curly kill him.
With the help of Curly Brace, Quote defeats Ballos and stops the source of the negative energy that was causing the island to fall, saving its inhabitants. Balrog saves the two before they are crushed by Ballos' collapsing prison; Balrog had been sent by Misery as thanks for breaking her curse. Quote, Curly Brace, and Balrog leave the island to live out their days in peace.