Having stipulated that the programme would only run for two series, the writers had to write an ending bringing together all threads from the two series. The final episode centres on a plot by coal miners, who, backed by hardened criminals, and led by a psychopathic convicted cop killer, aim to steal a large quantity of money from a train. Frank Morgan, introduced in the previous episode as a Police Officer more akin to Sam’s style of policing, plays a central role. Early in the episode, Sam comes to believe that Frank is the surgeon in the future, who has been talking to him through the television, telephones and in his head. Sam is told that a tumour in his head is keeping him in a coma, and thus in 1973. Sam surmises that Gene Hunt is the manifestation of the tumour in his dream state because Morgan tells him that he must destroy Gene in order to complete the ‘operation’ and come home. Morgan asks Sam to collect evidence to convict Hunt of gross professional misconduct.
Sam therefore tapes a variety of instances of Hunt abusing his power, including the beating of a suspect and the planning of an illegal sting to stop the train robbery. Sam meets with Morgan, presenting his evidence, and Morgan tells him that he is, in fact, not from the future, that the year is 1973, and that they both are part of an operation codenamed M.A.R.S. (Metropolitan Accountability and Reconciliation Strategy), the purpose of which is to secure better policing for Manchester. Morgan tells Sam that he is undercover inside Hunt’s A-division in order to bring his illegal activities to an end. Sam does not believe him, but Morgan tells him that, after his accident, his mind closed down, and he now suffers from amnesia. He tells Sam that his name is really Williams and that he has replaced this with his undercover persona. He shows Sam the graves of his ‘mother’ and ‘father’ and then ‘Sam Tyler’, all of whom have been dead since the 19th century. Disillusioned, he then looks at his police file and sees the note on his record about his transfer, signed by Morgan.
Meanwhile, work is progressing on the sting and Sam is disowned by A-division when he tells them that he is working undercover for Morgan. However, he must take part in the sting for it to be a success. Sam and Ray go undercover as security guards on the train, with Chris and Annie posing as BR staff. Gene is undercover as the previously-arrested gang member. Sam takes with him the radio Morgan gave him to call in backup. At the worst possible moment, the radio starts to crackle and falls out of Sam’s pocket, where it is seen by the gang members. Gene slams the door revealing his true identity. The gang members open fire on the train trapping the team inside. Sam tries to use the radio to call in Morgan, but without success. He then leaves the train to try and find help. In a tunnel he meets Morgan, who tells him that he would be content to let Ray, Annie and Chris die in order to bring Hunt down. Sam argues, but then is called into a bright white light calling him home. As he leaves, Gene, Chris and Ray are hit by fire from the gang members. Annie screams for help.
He wakes in his hospital room where Morgan tells him he could not remove all of the tumour, but that it was benign. Sam leaves the hospital’s Hyde Ward, room 2612 - explaining the references to ‘Hyde 2612’, and returns to his life as a 21st-century DCI. However, he quickly finds that he cannot relate to any of his colleagues, and even accidentally cuts himself without knowing. Remembering Nelson’s earlier observation that “You know you’re alive when you can feel,” he goes up onto the roof of the station. After looking out over Manchester, he takes a running leap from the roof, and appears back in 1973, just in time to gun down the gang leader, saving his colleagues, but subsequently ending his life in the present day. In the pub afterwards, Sam makes up with Ray, Chris and Phyllis, and goes outside in search of Annie. He asks her “What do I do, Annie?” and she says “Stay” (echoing their conversation at the end of Episode 1 of the first season). As they finally kiss, Hunt drives up with details of a new case. As they drive off, Sam hears, over the radio, voices in his native time, saying they are losing him. He changes channel, and, as the car drives off, Hunt and Tyler bicker as usual. At the very end, children run past and the girl from Test Card F follows them onto the screen, stops, and looks directly into the camera, before reaching out with her hand and “switching off” the television. It is debatable whether or not this signifies Sam’s death, or simply the end of the television series (the writer Matthew Graham has indicated the latter in an interview,[37] although the former has widely been inferred).
Ultimately the viewer is left with ambiguity as to which to emotionally accept as real: Sam’s life in the present day or his life in 1973. Has he really reawoken, and then thrown himself off a high building, presumably to his death? Writer Matthew Graham suggests so.[37] Or, as actor John Simm suggests, might this too merely be another one of his coma dreams?[37]. Back in 1973 Sam can still hear the voices that suggest he is in a coma but now he chooses to ignore them, possibly because he either thinks they’re symptoms of his delusions or because he doesn’t want to wake up. Either Sam concludes he had been suffering from delusions and paranoia brought on by amnesia and that his life in 1973 was real, or that he prefers to live in his imagination, or he doesn’t care which is real, only that he prefers 1973.
