The game begins with the protagonist, who tried to escape from Cyborgs using a jetbike. Unfortunately his vehicle got severely damaged and crashes in a jungle of Titan. He wakes up after a while, finds a gun and retrieves a holocube later on. His own hologram tells he is Conrad B. Hart, and he has to go find Ian in New Washington, telling he's not safe. After a little journey in the jungle, he meets Bolton, and asks to find his teleporter for medical assistance. After retrieving the teleporter, he teleports as he leaves his own ID card. After venturing for a while, Conrad meets Joe, he tells that New Washington is down the hole behind him, but an Anti-Gravity Belt is needed. To have it, he asks for several Grenada fruits. After swapping what they both want, Conrad jumps into the hole and activates the belt to safely arrive in New Washington.

Near Ian's place, he overhears a Cyborg interrogating him about a neurophage. After saving him, he gives a part of his memory back and gives a force field to protect him from bullets. Conrad then checks his GBI Virtual Reality with a virtual professor, who mocks him and tells him his own cryptic location. He finds a Memory Flash at the place, to find out about a deal with aliens in disguise in Death Tower. Conrad asks Joe a new identity for the Death Tower TV show. Joe tells the cost is 1500 credits, and points out the Administration Center to get a Work Permit for a salary. He uses Bolton's ID card to get a Work Permit. After doing his first job, he gets another Memory Flash, about a meeting between him and the real professor, telling him the Earth is being quietly invaded by aliens nicknamed Morphs. He then talks about a neurophage that he made to destroy them all. As he performs other jobs, he finds other pieces of his memory back as well as instructions to find the neurophage and its activator. With all the salary he got from performing jobs, he buys what he wanted from Joe, and enters the Death Tower TV show as Jay Carpenter.

After winning the show and getting a ticket to Earth, Conrad talks to the announcer about finishing up the deal. The disguised morph then reveals they have the new senator and Sonia, Conrad's girlfriend, and awaits them to be absorbed by The Mind. After killing the announcer, he uses the ticket to Earth to save Sonia and the planet.

Eventually, he is arrested in Earth's spaceport by corrupted cyborg cops, but manages to get out. He meets Ian again, who says that erasing his own memory to fool them didn't work, reminding him that he gave his first flashback, and reveals that he's a Morph, and the Morphs' goal: To perfect humanity as being a powerful entity. He gives to Conrad his painful last Flashback: showing that he had a very risky plan to go to the Morphs' homeworld. He then drives a jetbike, and asks Bolton where is the senator, and talks about the Paradise Club. When he goes there, he witnesses a meeting between the senator and the Morphs, who absorbed him, and talks about the Earth's colonisation. The vent where he stands for fell by his weight and is imprisoned by them. He manages to escape and meets Ian once more, and kills him. He finds a teleporter which leads him to their homeworld.

After being teleported, he frees the professor from his prison, and tells Conrad to get rid of an auxiliary brain so he can save Sonia. After that, he tells him to destroy The Mind, and use the neurophage in the planet's core. As he meets The Mind, it tries to persuade Conrad into being absorbed by him, only to get mocked at, and says he prefers being himself. After destroying it, Conrad releases the neurophage. As he tells Sonia that he's sorry, the professor tells Conrad to run as there is a spacecraft not far away.

Conrad manages to leave the Morph Planet alive as it explodes with the spacecraft. He tries to find where he is in the map, only to find out that his position is unknown. Unhappy, as he goes to his room, his holocube shows a hologram of Conrad congratulating him. Conrad then enters into suspended animation as the spacecraft goes. The credits shows the cutscenes, including one when the suspended animation ends as he wakes up. The post-credits cutscene is a discussion between some of the characters, with Sonia feeling that Conrad is still alive.