Sergeant Danny Waldron and his team of armed officers are deployed to detain Ronan Murphy, a suspect wanted in connection with a plot to commit a gangland execution. After Murphy's car is forced to stop, the suspect runs into a nearby housing estate, where Waldron corners him before the rest of the team arrive. Murphy surrenders his gun, but Waldron shoots him and manipulates the scene to make it look as though Murphy opened fire first. Waldron orders his team to discharge their weapons so as to avoid any trouble. Under interrogation from AC-12, Waldron remains cool until DS Steve Arnott's line of questioning into his private life begins to spook him. When Arnott confronts him outside, Waldron implies that he knows he will not get away with what he has done.

Supt Ted Hastings agrees to send DC Kate Fleming undercover as a new member of Waldron's squad in an attempt to uncover the truth. Waldron's team are tense as a result of being bullied into collaborating with Waldron, and Fleming identifies PC Harinderpal "Hari" Bains as the weakest link, but Bains refuses to testify against Waldron. After pressure from AC-12 department lawyer Gill Biggeloe, Waldron's team are returned to active duty. On their first call, they are tasked with raiding the home of a drug-dealer. Waldron pockets an illegal firearm, then stops Fleming just in time from accidentally shooting at a child who has been left in the house. Waldron demands Fleming transfer out of his squad.

Fleming attempts to provide first aid to the wounded Waldron, who dies in the ambulance. The remaining members of the team, PC Rod Kennedy, PC Hari Bains and PC Jackie Brickford, are interviewed by AC-12 and claim Waldron shot himself despite their attempts to stop him. Hastings attempts to arrest them, but Biggeloe convinces him to rescind the arrest. The police search Waldron's flat, finding Linus Murphy's dog (whom Waldron took with him after the murder to help lead the police to Murphy's body). Cottan discovers a box containing the stolen firearm, a photograph of a young Waldron and other boys alongside Ronan and Linus Murphy, and the envelope, addressed to Arnott, containing Waldron's list. Cottan destroys it.

Arnott agrees to take over the investigation of Waldron while Cottan focuses on his colleagues. Arnott locates Linus Murphy's home and finds his tortured and decapitated body, then finds the head in a storage room rented by Waldron. Waldron's team-mates find themselves suspected by their colleagues, and Fleming pressures them further by suggesting she knows they murdered Waldron, indicating she will tell AC-12 about a radio call Bains made to Waldron moments before his death, which was not included in the reports. Meanwhile, former DI Lindsay Denton has appealed against her conviction for conspiracy to murder Hunter, and Arnott is called as a witness. He denies having a sexual relationship with Denton, but the suggestion puts strains on his relationship with his girlfriend, DS Sam Railstone. Scared by pressure from Fleming, Kennedy demands to meet Bains in a disused warehouse, blaming Bains for their situation. This results in a brief physical confrontation. Denton claims in court that she had sex with Arnott.

Hastings authorises Fleming to begin surveillance of Bains. She watches him meeting with Brickford; when Arnott interviews Bains' superior, Bains panics and is observed calling his contact from a payphone. Fleming asks Cottan to organise a second examination of Kennedy's body, which Cottan intentionally neglects to do. The photo of Waldron and Ronan Murphy is traced to his time in Sands View boys' home. Arnott identifies Joseph Nash, another boy in the picture, and interviews him. Nash explains Linus Murphy was the caretaker at Sands View, that both men abused boys at the home, and that boys at the home were sexually abused by other men both at Sands View and at private parties. He identifies then-Councillor Dale Roach, but Roach is unable to stand trial, due to a stroke.

Brickford visits Fleming to find out what AC-12 has been asking her. Fleming reveals Bains has been making phone calls, seemingly to Brickford. Brickford confronts Bains, who cannot explain the calls. Brickford returns to AC-12 and confesses Waldron was shot in a struggle that Brickford and Kennedy were involved with. Only Bains saw how it began. Bains claimed Waldron had aimed at him, and that Bains grabbed the gun in self-defence. Brickford also confesses to lying about Ronan Murphy's death. Hastings has Brickford's police contract terminated and warns her she may yet be charged. Meanwhile, Arnott orders a second post-mortem on Kennedy's body. It indicates he was murdered. AC-12 moves to arrest Bains, with the assistance of a firearms unit, but his contact, Cottan, warns him and he escapes. He travels to the warehouse where Kennedy was hanged, and finds Cottan. As the firearms team approach, Cottan handcuffs and injures himself to fake a fight. Bains is arrested and the police find a noose, supporting Cottan's story that Bains was attempting to hang him.

Denton is taken to AC-12, where she demands a formal apology. She reveals she has a recording of herself and Arnott in a compromising situation that she will use against him as evidence of perjury if they do not comply with her requests. Denton is forced to work as a supermarket cleaner and later records an exploitative parole sponsor trying to pressure her into sex. Arnott, who is losing confidence within the department, meets with Denton and asks for help in finding the link between Sands View and Hunter.

Cottan is awarded with a commendation for his perceived bravery in arresting a corrupt police officer, Bains. He then proceeds to tell Biggeloe and Fleming he is concerned about Arnott's behaviour and that Arnott is carrying a firearm in his jacket. Bains confesses to killing Waldron on the demands of his unknown contact, but insists he did not murder Kennedy. Arnott and Fleming confront Hastings, saying they believe they should question a retired officer on the subject of allegedly reporting to a mother that a sexual-abuse complaint of Roach was dealt with, resulting in Roach being charged and sent to prison. The mother saw Roach in the newspaper some time later, so knew she had been lied to. The death of a former social worker at Sands View, ruled as a suicide, is reinvestigated due to allegations that he attempted to report the abuse to police and may have been murdered to prevent his case being pursued. They eventually interview former Vice Chief Superintendent Fairbank, who claims to remember no details of the case. He and Hastings share a handshake that Arnott identifies as Masonic.

Cottan continues to attack Arnott by pressuring PC Maneet Bindra to hold off on key forensics on the envelope found in Waldron's flat and then by spreading rumours surrounding Arnott's conduct, including telling Fleming he has a lead linking Arnott to Denton's bribe money. Arnott is eventually suspended by a hesitant Hastings, to whom he reveals the redacted file that would have linked Ronan and Linus Murphy to Hunter. Hastings challenges Biggeloe on this but is rebuffed. Meanwhile, Fairbank is called in for interview and maintains his ignorance as he is presented with images of alleged abusers. Joe Nash is shown a photograph of Fairbank, ostensibly to identify him as an officer that had overlooked accusations, but his reaction suggests Fairbank was one of the abusers.

Arnott and Denton investigate the possibility that Waldron hid another copy of his list of abusers. Denton surmises the list is kept digitally, so she tricks Arnott into pursuing a false lead while she, having stolen Arnott's pocketbook, goes to an internet cafe to access Waldron's emails. She finds a photograph of the list in his drafts folder and transfers it to hers as insurance.

Fairbank is arrested and interviewed on new information submitted by Nash during an identity parade. During the interview, Hastings receives the list sent by Denton which identifies Fairbank as one of the abusers. Meanwhile, Arnott awakens to find his pocketbook missing and his car stolen. As he reports the car missing, Hastings attends a call to a dockers' yard where the body of Denton has been discovered in Arnott's car. Arnott is arrested on suspicion of murder. During questioning, evidence identifying Arnott as 'The Caddy', such as money from Denton's bribe and the mobile phone he used to contact Bains, are shown to have been found in Arnott's gym bag. Arnott realises the evidence records relating to his signing out a firearm have been doctored to suggest he did not return it. He knows somebody within the department has set him up, but has no way of proving it. Cottan reveals that he has suppressed evidence regarding the envelope left by Waldron.

With authorisation from the East Midlands AC-3 superintendent, Fleming has been carrying out an undercover operation into the officers of AC-12. She highlights inconsistencies within Cottan's line of questioning against Arnott. Having spoken with DS Nicola Rogerson, she identifies Cottan as the one who fed AC-12 the doctored file on Ronan Murphy. Hastings confronts Biggeloe, who confirms it was Cottan who gave her the file. Bindra later reveals to Fleming it was Cottan who told her not to inform Arnott of the forensic findings of the envelope found in Waldron's flat. Fleming uncovers CCTV which confirms Arnott's car was driven on false number plates shortly before the time of the murder.

Cottan denies all knowledge of the doctored file and claims Arnott must have been the one responsible, having previously had a relationship with Rogerson. Hastings pressures Cottan on the suppression of the golf tee from evidence, as well as the fact that no blood was found on the tee despite blood being found on both the envelope and the list. Cottan claims he only removed it to prevent Arnott from becoming aware he was investigating him. Fleming reveals new forensic evidence against Cottan – fibres from the rope found at Kennedy's murder scene, in the boot of his car. Cottan strenuously denies any involvement with Kennedy's murder. Hastings probes him on evidence submitted by Morton, which suggests he pressured Morton into wrongly identifying 'The Caddy', and also used a secret mobile phone. Phone records reveal he previously called Hunter several times in the months leading up to his death. Fleming presses Cottan on the lead he claimed to have on Arnott linking him to Denton's bribe, which Hastings points out could not have been the money in Arnott's gym bag, as Cottan had made that claim the night before the money was discovered following Denton's murder.

Questioned about his whereabouts on the morning of Denton's murder, Cottan states that he was at home, but Fleming calls his bluff by implying that she might have visited the flat then and asks him to reaffirm his testimony. Cottan sends a text: "Urgent exit required", to three recipients, 'Removals', 'Talk', and 'Ride'. An armed officer guarding the interview shoots his colleague dead, then fires shots into the interview room, enabling Cottan to escape, and hands Cottan his pistol. Fleming takes the shot officer's weapon and deals with the other armed officer. She catches up with Cottan and dismisses the suggestion that they might have had a sexual relationship, telling him that all along she has been carrying out surveillance on him.