Stephen Baxter is on a night out to celebrate his old friend Judith's divorce. Outside the nightclub, he and Judith kiss and Stephen experiences a revelation. 40 days later, he stumbles dazed and weak off Saddleworth Moor. He reports that he is the son of God. He is taken to hospital. A Catholic priest photographs Stephen and sends the pictures to the Vatican.

Judith meets Johnny Tyler in a bar. They have been matched by a dating agency. She receives a telephone call from Fiona reporting that Stephen has turned up and she leaves, to the cynical Johnny's disappointment.

The police and the priest arrive at the hospital but Stephen has gone. The police raid Stephen's home and take away samples. After they leave, Stephen catches up with the priest. Talking in a café, the priest reveals that a hidden text has prophesised the second coming at this time and location.

Stephen visits Judith and both then meet Stephen's father, Frank, in the pub. On the way home, Stephen revels in his human senses. After he's left her, Judith encounters strange, threatening characters who seem to know about her.

The next evening, hundreds congregate in a football stadium after Stephen announces the second coming online. Stephen is joined there by his sceptical friend Pete. Judith leaves and goes to the pub, where she bumps into Johnny, a 'lost soul' in whom the devil is now manifested. Stephen creates a pillar of daylight encompassing just the stadium. Johnny runs home scared. Stephen's miracle is televised across the world.

Stephen makes a public appearance the next day. He states that mankind has made itself a god with technology, but ignored the teachings of the New Testament. A new start is needed. He announces that a third testament must be delivered to him in five days. Stephen is accommodated on the empty top floor of a police station. Judith remains sceptical that Stephen is what he claims. Thousands of potential third testaments are delivered to Stephen.

Judith visits a scientist analysing Stephen's miracle. Contrary to Judith's expectation, she believes act of God is the only explanation.

News breaks that medical investigations have revealed that Frank has been infertile for life, so cannot be Stephen's father. Stephen escapes the police station and meets Frank, Fiona, Pete and Judith in the pub. He invites them to join him in the police accommodation. A suicide bomb is detonated in the pub, but Stephen uses his powers to protect all those present, proving his divinity.

Judith, whose house is mobbed, goes to live in the police HQ with Stephen, as do Frank and Pete. They begin reading the thousands of third testaments received so far. Stephen reveals that he can die as he is human. He announces that judgement day, Armageddon and death await if there is no third testament. This is secretly filmed by the police chief and broadcast worldwide, leading to massed rioting. Johnny revels in the carnage.

Fiona's husband leaves her and she is gripped by religious hysteria. Stephen and Judith reveal their long-standing affection for each other and sleep together.

PC Lincoln, another lost soul, gives Frank drugs and a gun. Frank goes to assassinate Stephen but kills Pete instead. He is taken away by police. Stephen is placed under house arrest. Judith is taken home, but PC Lincoln redirects her to Johnny's house. Johnny states that Stephen will fall, without his friends around him. He hints that Fiona is in danger and Judith runs out.

At her home, Fiona prepares a lethal cocktail of drugs to take herself and her children to heaven. Judith gets there just in time to prevent her feeding the poison to the children.

Judith goes to her home, which has been trashed. She has a police guard. She phones Stephen and tells him that she knows what the third testament is. Stephen leaves the police station and crosses the devastated and deserted Manchester. Judith makes dinner for Stephen, mixing in rat poison. When Stephen arrives Judith reveals that the third testament is the death of god, a judgment on Stephen. They argue but Stephen ultimately accepts this fate, eats the poison and dies.

Six years later, Judith bumps into Johnny, who remains single, outside a super market. She has married her policeman guard and has a child.