Nearly two hundred years have passed for the Doctor since he left Amy and Rory in "The God Complex" and he is on a farewell tour of his friends as he knows he has only one day to go before his death (depicted in "The Impossible Astronaut"). He stops by Craig ("The Lodger"), who is living with his girlfriend Sophie in a new home and is raising their baby, Alfie. Craig, struggling to care for Alfie alone while Sophie is away for the weekend, suspects the Doctor is investigating something alien. The Doctor prepares to leave, but he notices a strange electrical disturbance in the area and decides to investigate.
Craig, while at a new department store with Alfie, discovers the Doctor working in the toy area. The Doctor reveals that he has traced the electrical disturbances to the store and is using the job to allow him to investigate further, hearing rumours of the disappearance of several store clerks and the sightings of a "silver rat". The Doctor and Craig enter a lift and find themselves teleported to a Cyberman spacecraft. A Cyberman emerges from the darkness and comes towards them but the Doctor manages to reverse the teleporter and disable it. As Craig returns home, the Doctor sees Amy and Rory shopping but stays out of their sight.
With Craig's help, the Doctor enters the store after hours and catches a Cybermat, which has been siphoning small amounts of energy to the spacecraft. The Doctor also encounters a malfunctioning Cyberman in the building's basement, and is curious how it arrived in the store. At Craig's house, while the two are distracted, the Cybermat reactivates, but they are able to stop it, and the Doctor reprograms the unit to track down the Cybermen signal.
The Doctor leaves on his own to locate the Cybermen at the store but Craig shortly follows, bringing Alfie along. The Doctor finds the spaceship actually sits below the store, underground, accessed by a tunnel from a changing room. The ship has been slowly siphoning energy from the store's power lines, reactivating its crew. The Doctor is captured by the Cybermen, who tell him that their ship crashed long ago but, with this new energy, will soon have enough power to convert the human race.
Craig, leaving Alfie with Val, follows the Doctor into the tunnel, and is also captured and placed into a conversion machine. The Doctor reveals his own impending death and urges Craig to fight, but the conversion appears to be complete. Alfie's cries over the closed-circuit television echo in the ship. Craig, encouraged by the Doctor telling him that this is his chance to be a father, fights and reverses the conversion. The rest of the Cybermen painfully experience the emotions they have repressed from Craig's struggle, and their circuits start to overload. The Doctor and Craig escape via the teleporter as the ship explodes, the blast contained by the cavern. Craig reunites with Alfie, while the Doctor slips away unseen. Craig returns home to find the Doctor already there, having used time travel to clean the house. The Doctor tells Craig that Alfie now has a much higher opinion of his dad. The Doctor leaves just before Sophie returns.
Nearby, the Doctor tells the TARDIS he knows this is his last trip in her and offers some parting words to a small group of children. In the far future, River Song, recently made a Doctor of Archaeology, reviews eyewitness accounts made by those children when they were adults, and also notes the date and location of the Doctor's death. She is interrupted by Madame Kovarian and agents of The Silence. Kovarian tells River that she is still theirs, and will be the one to kill the Doctor. Against River's will, they place her in an augmented astronaut's suit and submerge her in Lake Silencio to await the Doctor.
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