Sir Rex Farraday, of MI6, sits in a car watching a group of schoolboys running in a park. At a block of flats, armed police shoot dead David Thomas, a male nurse suspected of terrorism. A Daily Telegraph newspaper headline for 20 April 1996 reads 'Shoot to kill policy denied'. Farraday arrives at Harlech House, a Community Boys School, and looks up at a boy at a window before entering.

At a dockside two teenage boys climb into an abandoned vehicle. Armed police arrive and fire on the van, killing one of the boys and seriously wounding the other. One of the police calls for explosives. On a tape recorder a voice is heard saying: 'Oh God, what a balls up'. A Guardian newspaper headline reads: 'Police cleared of killing boy. Explosives found in van'.

Commander Jack Bentham is investigating the shooting of three female nurses at a demonstration when he is told by Deputy Commissioner Sir Harry Streeter he is to be seconded to investigate the alleged shoot-to-kill operations in the Welsh province. Streeter hopes there will be "no case to answer".

Arriving in Wales, Bentham tries to find if there is a link between the two shootings, but discovers duty logs and the tape recording have disappeared. Bentham's assistant, Detective Superintendent Frank Burroughs, tells him the Chief Constable has investigated complaints made by boys at Harlech House but found nothing in them. Bentham establishes a link between the shootings when he discovers that Stephen Fry, the boy killed in the van, witnessed Thomas being killed. He suspects Fry was killed to prevent him revealing that Thomas didn't have a gun, as the police claimed. Bentham starts an affair with Maureen Fry, Stephen's mother.

After meeting with a policeman who says he has information about the shoot-to-kill policy, Bentham tells Sir Cyril Llewellyn (Director of Public Prosecutions) that he believes Kit Davis, the other boy in the van, was the target, because a judge had sexually abused him at Harlech House.

Back in London, Bentham continues investigating the alleged rape of a woman by a policeman. Meeting up with a senior civil servant, he is told there is a tacit shoot-to-kill policy in each of the provinces, already demonstrated in Northern Ireland. He gets a call from Burroughs who says they've had a break-in.

Returning to Wales, Bentham is told that senior police officers want advance notice of his questions before agreeing to be interviewed. Meanwhile, someone is following Bentham around, recording and photographing his meetings. After learning that Deputy Chief Constable Donald Preece has stopped their inquiry into the shooting of a judge and that the Chief Constable won't allow him access to two MI6 agents for 'security reasons', Bentham asks what the point of his investigation is. The Chief Constable replies: "To prove there wasn't a shoot-to-kill policy".

After his police informant is killed, Bentham is told by an MI5 agent that MI6 was almost certainly responsible, and that MI6 had also stage-managed the murder of a previous Secretary of State because he was closing them down in the province. He gives Bentham a copy of a tape recording of one of the shootings. Tracing the chain of command, Bentham concludes that the Cabinet must have sanctioned the shoot-to-kill policy.

Farraday listens to a recording of Bentham talking to Burroughs and realises they're getting close to him. The MI5 agent tells Bentham that he'll fail if he observes the codes those in power expect senior officers to observe. He tells him to go for Farraday's weakness as a pederast. Maureen Fry is found dead, killed by gunfire from automatic weapons.

Back in London, Streeter tells Bentham that Farraday has AIDS. At a press conference, Bentham says the three nurses were shot because they were members of a terrorist group and that there is no substance to the complaints against the police. He refuses to answer a question about his shoot-to-kill investigation in Wales.