Sam Ryan assists the police in the investigation of a multi-vehicle collision that results in the death of 11 people. She is joined by two new colleagues: Dr. Leo Dalton, an experienced pathologist from Sheffield and Dr. Harry Cunningham. As they try to determine the causes of the accident, they find a severed arm that does not belong to any of the victims. They also have to deal with DCI Carol Deacon whose role in the investigation is not quite clear to them. Sam and Leo have somewhat different approaches to their job, particularly in how they deal with the police. Harry performs his first autopsy on a child.

The mystery of the severed arm is partly solved when the police discover a body floating in the river with a missing arm. The pathologists continue their investigation with little help from the police and DCI Deacon in particular. When she reveals to Tom that two of the men in the accident were undercover policemen, he realizes that Sam was correct and that he is being manipulated. The police refuse to tell them what is going on and Sam's interference has serious consequences. Harry continues to try and find a balance between detachment and compassion as one of the survivors of the crash seeks his assistance.

The team is called in after Mr. Stickley of the Police complaints Board feels that something is not right about an armed police raid on a house where several people were killed, including one of the officers and a mystery woman. A young Muslim called Melik has been badly wounded and lies in hospital. Mr. Stickley believes the policeman was killed by Rhys Allen, a colleague who was having an affair with the deceased's wife. Melik's sister Isra confides in Nikki that all the 'suspects' were unarmed and not terrorists and fears of a cover-up by the authorities are not helped by the aggressive attitude of Inspector Transfield, particularly when Nikki is attacked and evidence stolen from her laptop.

Harry Dalton and DI Helen Okoroafor manage to identify the dead woman from the scene of the raid - who turns out to be a DS who was working undercover and who the police refused to identify when the pathologists submitted her DNA sample to them. While DI Tranfield continues to search for the terrorist cell that he is sure is about to strike, Nikki Alexander continues to try and piece the evidence together from the scene of the raid but clearly there are pieces missing. A re-creation of the shooting shows her what happened and also identifies the only person in the right position to have shot the police officer.