The Doctor has come in answer to an advert for a lodger. He gives Craig paper bag stuffed with money (three thousand pounds is later revealed) and says he isn't sure if that is a lot or not. He seems more interested in who lives upstairs than seeing his room and generally behaves in an eccentric manner: air kissing Craig, raiding the fridge to make an omelette and telling Craig that he resembles a couch. He tells Craig that his luggage should "materialise" soon.
The TARDIS has attempts another landing, but fails.
The Doctor contacts Amy via an earpiece he wears throughout. She uses the phone to let him hear what the TARDIS engines sound like and he tells her that the thing that is stopping the TARDIS materializing is big.
While this is happening, a woman passes the house and hears someone asking for help. She enters, goes up the stairs and enters the top floor flat. Craig is taking to Sophie over the phone about the Doctor. She worries that with a name like that and three thousand pounds in cash he might be a drug dealer. The local area is hit by a time loop. The Doctor tells Amy to pull the zigzag plotter to keep the TARDIS steady and then says he needs to get some important things. He leaves the house and returns later with a shopping trolley full of junk.
The next morning, the Doctor is in the shower. Craig hears a big bang upstairs and goes to investigate. The Doctor leaps from the shower, grabbing Craig's toothbrush instead of his screwdriver. A man in the flat above tells Craig he doesn't need his help. The Doctor, wearing only a towel, rushes into the hallway just as Sophie arrives. Craig takes a phone call and finds that his pub league team is short of a player. The Doctor assumes that this is a drinking league but when he finds that it is football he offers to fill in. He tells Amy he is doing this to appear more 'blokey' but asks her if football is the "one with the sticks".
The game is played on a local parks' pitch. Initially, the Doctor seems confused about what the team captain is saying to him but once the game starts he is exceptionally talented and scores a large number of goals. Afterwards, he misinterprets one of the team saying they can annihilate other teams. He quickly realises that this was just a figure of speech. Meanwhile, another woman is asked to enter the upstairs flat by a little girl. As she screams in pain or fear at whatever is in there, the team are caught in a time loop and the TARDIS suffers massive turbulence. The Doctor steps out of the time loop and tells Amy he is worried the TARDIS could be lost in the Time Vortex.
Back home, Craig tells the Doctor Sophie is coming round and he wants to tell her his true feelings. The Doctor says that they won't know he is there and withdraws to his room to work on something. Sophie notices that the stain on the ceiling has grown even larger. Craig tries to tell Sophie how he feels about her but the Doctor appears from behind the couch wanting to know how to switch a (regular) screwdriver on. He ends up joining them, tangled in wires for his scanner. Sophie tells the Doctor about her dream of travelling abroad to care for animals. He gets Sophie to admit she doesn't want to stay working in a call centre. After she leaves, the Doctor enters his room, where the scanning device is complete. He tries to locate the problem above but the results are inconclusive so he tells Amy to look up the blueprints of the building. Craig touches the stain on the ceiling but seems to receive some kind of shock from it.
When the Doctor takes breakfast into Craig he finds him seriously ill. He uses old teabags to start his cure. Craig is distraught: he has to be at work for an important meeting but the Doctor tells him to rest as he is too weak to go. When Craig wakes up it is afternoon. He dashes to work, only to find the Doctor at his desk. The Doctor is dealing rudely with a client on the phone. Craig's boss is delighted with the Doctor's contribution to the meeting that Craig should have attended. Just like with the football match, Craig is dismayed at how easily the Doctor succeeds and usurps him. Sophie asks Craig for his opinions about her leaving to work abroad but he is too distracted to listen and says that it is fine with him.
Back at home, Craig goes into the Doctor's room to see what he has been doing and discovers a massive contraption, the scanner, made out of household junk. He sees the Doctor talking to a cat about people who go up the stairs but never return. He decides it is time for the Doctor to leave. The Doctor tries to explain that he can't go now but Craig won't understand him so the Doctor headbutts him. This gives Craig an instant telepathic history of the Doctor. A second butt explains his investigation of the flat above. Sophie arrives but a little girl upstairs calls to her for help. A time loop begins and Craig is now able to feel it as an outsider. He and the Doctor realise that someone upstairs is in danger and rush off to help. Amy calls the Doctor to tell him that, according to the plans, the house is a bungalow with no upper storey.
When they step into the upstairs flat they find a large, incomplete TARDIS-like interior. Sophie is being dragged towards the console by an invisible force. A man appears: he is a holographic auto-pilot. He tells them that the ship has crashed, the pilots are dead and a program has been trying to find suitable replacements. Because humans aren't able to withstand the energy in the program they have all been burnt out. The Doctor cannot believe that the ship is trying to use humans as replacement pilots but it immediately tries to force him to touch the controls. Amy says that should be a good because the Doctor isn't human but he replies that his partaking in the test will blow up the solar system.
The Doctor deduces that Craig was not wanted by the ship because all he wanted to do was stay in his flat with Sophie. The auto-pilot detected people who yearned to leave, as did Sophie on this occasion. When the Doctor points out how much Craig loves her, Sophie reciprocates and kisses him. Neither of them wants to leave now and when they touch the console the ship begins to shut down and implode. As they run from the control room they see the bungalow for what it is, albeit with a ship on the roof. Passers-by in the street still do not see because of the perception filter in use.
The Doctor tries to leave unobtrusively while Craig and Sophie are romantically distracted but Craig catches him as he is going. When the Doctor says he will come back Craig knows it is not true but gives him the keys to the flat anyway. The Doctor makes his exit without seeing the crack behind the fridge that resembles the one in Amy's bedroom.
Back in the TARDIS, the Doctor and Amy prepare the note for the paper shop window that the Doctor will answer to get the flat. Amy asks if the Doctor for a pen and while she looks for one in his coat pockets she her engagement ring.
