Craig tells the Doctor that this weekend is all about proving that he can cope on his own, which he can't. The Doctor shushes Alfie (who, he reveals, prefers the name Stormaggedon, Dark Lord of All). The Doctor adds that he is on a farewell tour and has only popped in to say hello. As he strides away from the house he determinedly ignores the flickering street lights. However, he can't help scanning the area and notices a patina of teleport energy.
The next morning, Craig is shopping in the department store when he finds the Doctor working in the toy department. Craig immediately concludes that the Doctor is investigating something alien and dangerous. The Doctor says that three people have vanished in the past week from the local area. He also has seen that teleport energy is being used. As he says this he leads Craig into a lift that has been taped up and has a "Danger" sign on the door. He says that the teleport device must be disguised as something but he can't figure out what. They promptly arrive aboard a space ship with a Cyberman closing in. The Doctor uses his screwdriver to take them back to the shop. He tells Craig that he has fused the teleport so that the Cybermen are stuck in space.
The Doctor tries to make Craig leave but he refuses, saying that it is safer to be near the Doctor in these circumstances. The Doctor tells Craig to go round the store and see if he can spot anything unusual. This leads Craig into trouble when a shop girl thinks he is a pervert. However, the Doctor arrives to smooth things over. He has been told about a silver rat that has been seen in the store. When the shop assistant mentions that Shona has not turned up for work and the last time she was seen she was on her way to the changing rooms he decides to head there. When the sonic screwdriver reveals that Shona was taken by a Cyberman, Craig is puzzled because he thought they were looking for a rat. The Doctor tells him that the thing is a Cybermat and it has been sucking energy from the store.
As Craig goes off to change Alfie's nappy, the Doctor turns and sees Amy and Rory walking through the shop. A little girl walks over and asks for Amy's autograph and the Doctor sees Amy's face on a hoarding, advertising Petrichor perfume, "For the girl who is tired of waiting."
After the shop closes, the Doctor and Craig hide behind the aisles. The Doctor nets a Cybermat but as he celebrates he hears George, the security guard, scream in the basement. The Doctor races down and sees George's corpse. A Cyberman steps out and chops the Doctor with its arm. Craig finds him lying unconscious. He says that he would have been killed if the Cyberman didn't have a damaged arm. He says that George will have been taken, like the other missing people, for spare parts but he wasn't taken because he is not compatible. He is puzzled about a number of things: the Cybermen's ability to beam down after the teleport was fused; the need for spare parts; the damaged Cyberman.
The Doctor returns to Craig's home to work on the Cybermat. Craig goes out to get some milk and the Doctor is left holding the baby. The Cybermat reactivates and the Doctor ends up running from the house with Alfie, accidentally locking himself out. Craig returns and is attacked by the Cybermat. As he fights it off, the Doctor crashes in through a glass door and helps Craig subdue the Cybermat. Afterwards, as the Doctor wipes the Cybermat's brain, he confesses to Craig that he shouldn't have come here, and by being there he has put Craig and Alfie in danger. He goes on to tell Craig that he is leaving, his time is up and he is due to die the next day. When he turns to see Craig's reaction he finds both man and baby are asleep.
The next morning, Craig wakes up on the couch to find that the Doctor has returned to the store with the reprogrammed Cybermat to stop the Cybermen. Craig follows after the Doctor with Alfie. The Doctor realises the Cybermen's ship is not in space but has been buried beneath the Earth for centuries and is beneath the store. They climb up to a door in the changing room. Craig arrives and leaves Alfie with a middle-aged shop assistant, Val. He follows the Doctor into the tunnel, armed only with a barcode reader. The Cybermen are telling the Doctor, who they have taken prisoner, that they plan to take over the Earth, even though there are only six of them. When Craig arrives they disarm him and say he will be the new Cyber Leader. He is put into a conversion machine. The Doctor releases the reprogrammed Cybermat but one of the Cybermen simply treads on it.
The Doctor urges Craig to fight the conversion but it appears to succeed until Craig hears Alfie's cries from the CCTV in the ship. Craig fights the conversion and the Cybermen overload as they feel the emotions they have repressed. Their heads begin to explode. The Doctor and Craig use the teleport to get away as the ship explodes. Craig is reunited with Alfie while the Doctor concludes that Craig "blew them up with love." When Val assumes that they are a couple, Craig tries to deny it but the Doctor has already slipped away.
When Craig returns home he finds that the Doctor has used time travel to clean the house throughout and got a glazier to fix the door. He is waiting for Craig and tells him that Alfie prefers to use his real name rather than Stormageddon and is very proud of his dad. Craig is worried that the Doctor is in trouble but the Doctor insists he has to leave for America. He borrows some blue envelopes from Sophie's stationery drawer. Craig gives him a Stetson hat as a parting gift.
The Doctor leaves by the back door as Sophie enters at the front. Craig reassures her that nothing weird has happened while she was gone, but Alfie says, "Doctor".
Before he enters the TARDIS the Doctor speaks to a small group of children. In the distant future, River Song, newly made a Doctor of Archaeology, reads over the statements written by those children. She also has the date and location of the Doctor's death. Madame Kovarian steps out of the shadows. She says that River won't remember her because of the things they have done to her head. Two Silents accompany her, and Kovarian introduces them as River's "owners". As soldiers arrive with an astronaut suit she tells River that she will be the one to kill the Doctor. They sedate her and place her in the suit. She is submerged in Lake Silencio to await her fatal meeting with the Doctor.