Steven Baxter, a good-hearted but slightly dim video shop worker from Manchester, disappears for forty days and forty nights after a drunken night out with his friends, during which he shared a kiss with his best friend Judy. He is found wandering Saddleworth Moor, and he claims to be the second coming of Jesus. At first he is met with scepticism, and is even locked up. One of the few people who believes him is a young Catholic priest, who mentions an obscure Christian text that mentions that the lamb will be sent to the city of the North, followed by a series of numbers that turned out to be map co-ordinates. The recent death of the Pope is also seen as a sign. Steve escapes and, after one final night out before starting his duties, decides to indicate he is really the son of God to humanity by turning night into day over the small area of the football stadium at Maine Road (he lets people know about it by advertising on the internet). The feat attracts the attention of the world's media. Steve then announces he must find the third testament within five days. He states that humanity needs to start taking responsibility for their actions, and that everyone, regardless of their religion or origin, needs to begin again and forget past conflicts. He also says that Christians shouldn't boast about being right, then reveals that currently Heaven is empty, while Hell is bursting to the seams. There is much hysteria and panic; particularly when The Devil and several demons possess people (only indicated by silver eyes) to cause trouble. Satan takes possession of a man named Johnny Tyler that Judy met through a dating agency. He eventually reveals to Judy he wants Steve to fail and fall into despair, so that after Armageddon God will judge Steve's actions as a human and send him to hell, and they can rule together. In a deleted scene, it is revealed Satan also wants God to return to being the merciless, angry God of the Old Testament.

Later we discover Steve's earthly father couldn't have fathered him as he was born sterile, another indicator that Steve is really the son of God.

There is also media frenzy surrounding the events, especially after a tape is leaked of Steve saying that the world will end if the testament isn't found, and he is taken into police protection. Some of Steve's friends accept him as the Messiah - Pete (who kept his Christianity hidden, not knowing how his friends would react) and Fiona (who becomes crazed, as this is the first time she's ever believed). Judy (an atheist), remains sceptical. She and Steve have some heated arguments (at one point, in a fit of anger, Steve is tempted to use his godly powers to kill her), especially as despite being the son of God, Steve is neither omniscient (relying on information "downloading" into his head, which frustrates him too) nor omnipotent (e.g. he can't heal the sick). Steve later says that he does have powers, but he refuses to use them as he could get power mad, and reiterates it's up to humanity to sort themselves out this time. Judy is also confronted by several demons and manipulated into situations to get her to believe, which is part of Satan's plan to have Steve fall into despair.

During the next few days, Steve miraculously survives several attempts made on his life, including a bomb going off in a pub he's in. The devil and his demons also attempt to turn his father Frank against him, getting him hooked on drugs and alcohol and convincing him that he is now a joke in the public's eyes. Frank tries to shoot Steve, but ends up killing Pete. After her husband leaves her, Fiona attempts suicide and tries to kill her children too. Also during this time Judy and Steve's relationship grows deeper, and they make love.

Steve himself has no idea what the third testament will be; he receives too many candidates to figure out which one is the real one. The Chief Superintendent of the police, who is also possessed by a demon, has them thrown out, saying that even if it was there, Steve won't be able to make his broadcast to the world. Having failed to discover the Testament, the people of the world hide in their homes, fearing the world's end.

Steve then visits Judy in hope of trying to work out what the testament is, and Judy reveals to him that it is the record she is making of events. Judy, who is filmed night and day by cameras from the world's media around her house, makes spaghetti and laces it with rat poison, but announces this to Steve before presenting it to him. She states that it is Judgment Day, but for Steve and God, stating that it has been the existence of God or the argument about it which has led humanity to do so many bad things to one another. Steve is persuaded by Judy that he must die, and moreover make it permanent (in the sense of ceasing to exist rather than returning to heaven), so that humanity fights for itself rather than relying on the evils of fundamentalism. This will not only be the death of him, but of God, Satan, Heaven and Hell - the end of all religion. She also says that the absence of any kind of afterlife may scare people into living their lives properly.

Steve doesn't believe her at first, thinking she was influenced by the demons. He does one last divine "download" and, to his horror, realises that this is indeed the Third Testament, "the closing of the family business." He is scared at first, but then decides that it is time to die, and he eats his Last Supper. Henceforth, the world goes back to normal, with a few people referring to Judy as "the woman who killed God", but she otherwise goes back to living an ordinary insignificant life, having married the policeman who guarded her despite everyone else leaving their jobs and posts in fear of the apparent apocalypse. Judy sees Johnny Tyler (who has no memory of being possessed) and asks him if she did the right thing, but he can't answer (suggesting that the audience needs to decide for itself whether she did or not).