The TARDIS materializes in a park and the Doctor emerges. Some force shoves him out and the TARDIS dematerializes with Amy struggling at the controls. She's able to confirm they are on 21st century Earth for him but then discovers that the TARDIS has departed and left the Doctor behind.
One day later, a boy is passing a house on Aickman Road. A man calls to him through the intercom and says there's been an accident, and he needs help. The door opens and the boy goes inside and up the stairs. An old man at the top says something terrible has happened. When the boy enters the upstairs flat, the door closes behind him.
In the flat below, Craig Owens and his friend Sophie are talking when she notices a stain on the ceiling. He dismisses it as nothing and they go to watch television, unaware that the stain is visibly growing. They hear noises from above and the lights flicker. Craig tells Sophie that he has put an advertisement in the papers for a flatmate and she gets a call to deal with a friend. She apologizes for leaving him despite the plans they had for pizza, and he insists it wasn't important. As Sophie goes, she hears more noises from upstairs and catches a glimpse of someone watching her through the door.
Inside, Craig considers a photo of him and Sophie together and debates telling her that he loves her. The doorbell rings and he goes to answer it, rehearsing his speech, and comes face-to-face with the Doctor, who informs him that he's the new lodger. The Doctor takes Craig's keys, as Craig wonders how he knew where the address was when he hadn't put it up yet. When Craig hesitates, the Doctor hands over a bag full of money to pay the rent and goes inside. He asks about the upstairs lodger, and Craig admits he doesn't know much about him. The Doctor takes an immediate interest in the rot stain and then asks to see his room. As Craig explains that the owner, the previous occupant, inherited money and moved out suddenly, there are more noises from above and the Doctor agrees to take the room.
The Doctor begins cooking an omelette and asks about Sophie. Craig insists that nothing is going on and goes on about his business. The Doctor explains that his stuff will materialize eventually, if everything goes according to plan.
The TARDIS tries to land in the park without success.
After eating, Craig begins to realize that the Doctor is a bit strange. He admits that he's not much of a traveler and insists that he likes London. The Doctor notices that he's fondling his keys, and Craig gives the Doctor his own keys. In response, the Doctor warns Craig not to touch the rot on the ceiling.
Once he's alone in his bedroom, the Doctor contacts Amy via an earpiece.
Craig calls Sophie and admits that the Doctor is rather weird. Sophie suggests that he's a dealer.
A woman is passing outside when the man in the upper flat calls out to her and says he needs help.
Amy admits that the TARDIS is acting strangely and the Doctor realizes that something in the flat is preventing the TARDIS from landing.
The woman goes to the upstairs flat.
The Doctor warns that something capable of affecting the TARDIS is scary big, and Amy wonder's if he's scared.
Craig hears the Doctor seemingly talking to himself. Meanwhile, the Doctor explains to Amy that he can't give himself away to whatever is upstairs, so he'll have to pass himself off as an ordinary human being. The TARDIS tries to materialize again and the Doctor notices that the nearby clocks are indicating a time loop. Upstairs, power fluctuates while the woman screams in terror. The TARDIS stabilizes and the Doctor gives instructions on how to protect herself. He then goes out and collects some items from around the neighborhood.
The next day, Craig waits for the Doctor to get out of the shower. Meanwhile, there are more noises from upstairs and Craig goes upstairs to investigate. The Doctor doesn't hear him over the water. Craig goes upstairs and knocks on the door. The old man inside opens the door. Meanwhile, the Doctor realizes that something is wrong, trips over the curtain, and reaches for a toothbrush. The Doctor, naked except for a towel, arrives at the stairs and Craig insists that everything is fine. As Craig goes to answer the phone, the Doctor proceeds halfway up the stairs. Sophie comes in and the Doctor introduces himself. Craig informs him that there's a football match today and they're one short. The Doctor agrees to help so that he looks like a normal bloke, and Craig and Sophie argue about whether it's a date. Even the Doctor realizes there's something going on between them. He also realizes that Sophie has her own set of keys and figures she likes it there, too.
As the Doctor dresses, he tells Amy what he's doing to blend in. On the way to the park, the Doctor explains that he's simply called the Doctor. The rest of the team meets tem and the Doctor begins playing. The Doctor is incredible, managing to upstage Craig as everyone cheers.
Back at the flat, an older woman is passing when a young child calls through the intercom and asks for help. The woman goes inside and finds a young girl at the top of stairs. She goes upstairs to help and follows the girl inside.
The team celebrates and the Doctor notices that they are all caught in a time loop. He runs off to the flat and confirms with Amy that the TARDIS is having problems again. She reports that there are 9s on the monitor before screaming. The Doctor confirms that she's safe and warns that the TARDIS could be lost in the vortex forever. The monitors now show 5s, and the Doctor assures her that things are safer for the moment. He tells her he has some rewiring to do.
Later, Craig stops by the Doctor's room and informs him that Sophie is coming around that night. He wants the Doctor to give them some space. There are more noises from upstairs and the Doctor assures him that he won't know he's there. He then goes into the room and back to work.
When Sophie arrives, they observe the stain, which has grown, and Craig suggests they stay in. She turns off her cell phone and he hesitantly starts to suggest something. The Doctor pops up and explains that he's reconnecting all the electric switches. Craig insists that he leave, but Sophie invites him to stay and have a drink. She tries to talk to the Doctor and starts telling him things she'd never tell Craig. The Doctor points out that they both have dreams but aren't acting on them, and Sophie takes offense at first. She then realizes he's trying to provoke her into figuring out what's really keeping her there. She and Craig both wonder what is keeping them there.
As Sophie goes, Craig wonders if she's leaving to see the world, and he wonders what is keeping her there. Sophie doesn't have a ready answer. They hug and she leaves for the night. As Craig goes inside, the lights glow in the flat above.
In his room, the Doctor makes a construct out of the neighborhood debris but doesn't detect any advanced technology upstairs. He has Amy get him the blueprints for the building and then goes to recruit a spy.
In the flat, Craig notices that the stain is growing ever larger. He climbs up and touches it, ignoring the Doctor's warning, and is burned.
The next morning, the Doctor brings Craig breakfast in bed. He discovers that Craig is sick and realizes he touched the stain. He manages to revive him, and assures Craig that he is important. Craig wakes up later and realizes that he's late for his important planning meeting. When he arrives there, he discovers that the Doctor is there, took over the planning meeting, and got rid of an obnoxious client. Sophie informs Craig that she's decided to take a job studying monkeys and travel the world. Craig's boss is thrilled to have the Doctor there. Craig, angry, goes back to the flat and sneaks into the Doctor's room. He finds the spinning device.
When the Doctor returns, he spots a cat coming downstairs. He talks to it, and Craig watches through the peephole. He goes outside and tells the Doctor to go. When the Doctor wonders what is going on, Craig explains that the Doctor has destroyed his life and found the gizmo in the bedroom. The Doctor insists that he has to stay, but when Craig refuses, the Doctor bumps his head to Craig's and shares some of his memories. Craig realizes that the Doctor is an alien. The Doctor then shares him memories of recent events, and shows him Craig's advertisement... sent to him from Amy in the future.
As Sophie comes inside and uses her key to open Craig's door, a young girl calls to her from the top of the stairs and asks for her help. Sophie goes upstairs to investigate.
Amy is still searching for the plans, while the Doctor explains that he's shared the cat's psychic impressions. The intruder upstairs is burning up people for whatever he does, which causes the strain to grow. They hear more noises and the Doctor realizes the time loop has started again. As the TARDIS begins to convulse again, the Doctor realizes that someone is dying upstairs and runs to investigate. As Craig goes after him, they spot Sophie's keys in the door and realize she's the next victim. They run up to the door but Amy yells at them to stop. She warns them that she has the plans, and it's a one-story building. They open the door and discover a vast chamber and a TARDIS-like structure. The Doctor realizes that someone is trying to build a TARDIS.
Sophie is being pulled toward an activator on the central console. The Doctor and Craig manage to stop her, and the Doctor spots other corpses. As he approaches them, an image of a man appears and says that help is required. The Doctor realizes that it's a hologram, the emergency crash programme, and it's been luring people up to try them to find a suitable pilot. However, human brains aren't strong enough to handle the strain. The programme informs them that it has killed 17 people and will continue testing everyone on Earth. However, now it has found the correct pilot, the Doctor. It pulls him toward the console, and the Doctor warns that his energy will overload the device and cause a massive explosion.
As the Doctor tries to resist, he tries to figure out why the programme only took Sophie today. He concludes that she's decided to escape, and that if Craig touches the activator, his refusal to escape will cause a backlash. Craig does it and the Doctor is freed. He tells Craig to think of everything that keeps him from leaving, and Craig declares his love for Sophie. She says that she loves him as well, and the Doctor tells them to kiss. When they do, the TARDIS is freed. The programme breaks down as it goes into emergency shutdown. They all run out of the flat and look up to watch as the second floor disappears, revealing the alien vessel. It disappears, leaving a one-story flat in its wake. Thanks to the perception filter, nobody realizes that anything has happened.
Later, Sophie and Craig are kissing and he explains that he'll go anywhere to be with her. The Doctor comes in, realizes what they're doing, and quickly turns around. He leaves his keys on the table and tries to slip away, but Craig and Sophie realize that he's there. Craig gives him the keys, realizing the Doctor won't return but wants him to have them as a token. The Doctor congratulates them and leaves... unaware that the time crack has spread onto the wall of the flat.
Back in the TARDIS, the Doctor tells Amy to go back in time and leave the note for him. She suggests that he find her a fellow and play matchmaker again. As she gets a pen from his jacket, she finds Rory's engagement ring and starts to remember the crack... and Rory.