The game is set in the year 2044 in downtown New York City, in a future with many Orwellian influences. The player plays an advertising agency worker named Peter Wright, who is depressed and drinking heavily after the death of his wife and child in a terrorist attack. One night, as he is drinking, he hears a commotion in the hall. Looking out through the peephole in his apartment door, he sees a SWAT team storm the apartment of his next door neighbor and carries out a middle-aged man, much to the pain and anguish of his wife. Peter learns that the man was a freelance journalist named Graham Oswald, and is asked by his wife to discover what had happened to him.
Attempting to investigate, Peter is deflected at every turn by the police who begin to investigate him, a branch of Luddites, and even online acquaintances. Eventually, Peter is informed he's won a "Vacation" to an orbiting station which is a cover for a rehabilitation clinic, and he meets a number of intellectual and political figures who've been removed from society, as well as a factory of automated drones. Peter sabotages the drone factory and escapes the station, and is sent to prison on Governor's Island, the only inmate but learns Oswald was recently there. Peter removes a tracking implant he is surgically installed with and escapes by swimming to shore.
Escaping underground, Peter discovers a dying Oswald, who is on his last legs after a harrowing escape from a prison on Governors Island. Before dying, Oswald tells Peter that he must go to Alaska and complete the mission that Oswald failed. After Peter arrives in Alaska, he discovers that the government is being run by a dystopian artificial intelligence, whose only concern is keeping the world tidy and in order and has slowly begun to erase evidence of its existence. IT also reveals that it has been watching Peter for a long time, and is several of the online friends he has and that the computer engages in massive social manipulation. He further threatens Peter that if it is deactivated, it will launch a set of nuclear weapons, including one at Peter's home. Peter successfully shuts down the computer system and manages to abort the launches. In the epilog, Peter's computer pops up with a message from an online contact, asking if Peter wants to be friends.