Galerians starts with Rion, a young 14 year old boy. He is strapped to what seems to be a medical examining table. He uses his newfound psychic powers to release himself from his restraints, and to open the door. Rion has no memory of his past, but he does know that he wants to be free. He runs out into the hall and fights numerous guards and scientists along the way out. Rion also stumbles upon a few strange things. When he uses his powers, he can sometimes see past events. For example, when he scans a chair, he sees a distorted being sitting in it shaking eerily. He continues on and sees a row of tubes. Inside the tubes are what appear to be fetus'. Rion is shaken but continues on his escape nonetheless.

Rion eventually makes his way up to the Clinic Chief Lem's office. The old man demands that Rion return to his room, but Rion refuses. They fight and Rion wins by using his psychic powers. Lem dies and turns to his true self, a machine. Rion learns that he was a Galerian. Rion takes the red jewel that is in Lem's one eye socket and holds it up to the machine that opens the door. Rion gets in the elevator and rests his head against the side, angry and confused about everything that has happened to him so far. He also expresses fear at being all alone in Michaelangelo City.

Rion eventually makes his way to his home. (How he knew where it was, I have no idea). He enters through the side and wanders through the immense house. There are many enemies in his home he is forced to fight. Rion sees telepathic images of his parents and their grisly deaths. Rion eventually stumbles upon an old machine that generates his father's last message to Rion. He tells him of how he created Dorothy, the super computer, with his friend Dr. Pascalle. Dorothy eventually became too powerful and they couldn't find a way to destroy her. They came up with an idea: the virus to disable Dorothy would be planted in Dr. Pascalle's daughter Lilia's mind. The key to activate the virus would be hidden in Rion's mind. Mr. Steiner entrusted the fate of the world with his son. He apologizes but says that there is no other way. He also tells Rion to find Lilia so they could defeat Dorothy. Lilia's old doll is located in the shed of the Steiner's home. Rion finds it and makes contact with her. She is happy that he finally answered her calls, just like her father said he would. Rion promises to find her and protect her. As he tries to leave, a Galerian named Birdman reveals himself. They fight and Rion wins. Birdman tells Rion a bit more about the Galerians and tells him that he should be afraid of himself. After he dies, Rion feels bad that he killed him but continues on to the hotel Lilia is at anyway.

Rion heads over to the Babylon Hotel. He goes through a lot of peoples rooms, with no real purpose, eventually meeting and killing Rainheart and finding Lilia. Rita, a Galerian, comes to "bash her brains" but Rion isn't having any of it. He fights her and she kills herself, much to Rion's disdain.

Lilia is happy to see him and they leave for the Mushroom Tower together. This is the final area of the game, where Rion and Lilia plan to destroy Dorothy. They make their way to the top, where Rion meets Cain, his double. Cain claims that Rion is his twin, that they are both Galerians created by Dorothy. They fight and Cain dies.

Lilia and Rion go over to Dorothy and she tries to get Rion to kill Lilia. He refuses and Dorothy says that Rion was her biggest failure and she is ashamed to have created him. Lilia and Rion send the virus and destroy the evil computer. As Dorothy dies, she apologizes for being an awful "mother". Whatever. Rion falls into Lilia's arms, dying. (I guess from either the battle or using all those drugs). He tells her to just let him die and to escape. He then asks her if he was the real Rion and she says that he is. He then dies in her arms and the game ends.