The game centers on Jonathan Ingram, one of the five "Policenauts", astronauts with police training, assigned to ensure the safety of Beyond Coast, mankind's first fully functional space colony in the year 2013. Johnathan tests a new space walking suit, but is drifted away into space by accident and is presumed dead by his colleagues. He is found alive and well 25 years later thanks to the cold-sleep module connected to the suit. Three years later, Jonathan (now a private investigator working in the former Los Angeles) is visited by his former wife, Lorraine who asks for Jonathan's help in solving the disappearance of her current husband, Kenzo Hojo, the only clues he left behind being a torn leaf, a set of capsules, and the word "Plato". Jonathan is reluctant to take her case at first, but after Lorraine leaves his office, she is attacked and murdered by a man in a black motorcycle suit. Jonathan, unable to catch the culprit, decides to fulfill his ex-wife's final request and travels to Beyond, where he is reunited with his former partner from his LAPD days, Ed Brown who agrees to help Jonathan investigate the circumstances surrounding Hojo's disappearance and Lorraine's murder.

During the course of the investigation, Jonathan and Ed learn that Becker and Tokugawa have been involved in running an illegal drug and organ trafficking ring in order to counteract the negative side-effects of being in space for long periods of time. Hojo had been included in the business in order to save his daughter, Karen, and ultimately wanted to leave, only to be murdered. During a stand-off with Becker, Jonathan records Becker's confession about the scheme and has Meryl broadcast the recording live, exposing the scandal to the colonists. Ed saves Jonathan from death, while Meryl and the remaining police arrest Tokugawa. Jonathan donates his bone marrow to Karen upon learning that he is her biological father, and returns to Earth.