After stepping out of the TARDIS in modern-day Colchester, the Doctor is blown off his feet by a blast of air, and the TARDIS, Amy still inside, dematerialises into the time vortex and refuses to rematerialise. With Amy's help, the Doctor tracks the disturbance to the second floor of a house. The Doctor opts to take a room for rent offered by the downstairs tenant, Craig Owens, in order to determine what is present on the second floor without alerting whatever it is to his Time Lord nature. Neither Craig nor the Doctor are aware that people are being lured off the street to the second floor flat and never leaving again, but the Doctor is conscious of localised time loops and disturbances aboard the TARDIS that coincide with noises from the second floor.
Over two days, the Doctor attempts to adapt to human life. He learns about Craig, an office worker with little aspiration to move onward. Craig is stuck in a platonic relationship with his co-worker, Sophie. The Doctor becomes overly involved in Craig's life, becoming the star player in Craig's local football club, filling in for him at the call centre when Craig falls ill, and encouraging Sophie to follow her dream of traveling overseas to help animals. Craig, who has not yet professed his love for Sophie, becomes upset; he accosts the Doctor and demands that he leave, which forces the Doctor to reveal his history and his reason for being in the flat.
Sophie arrives while they argue and is lured upstairs; the Doctor and Craig follow, learning from Amy that Craig's building has never had a second floor. Inside, they find an alien ship housing a primitive time engine. The ship crashed some time ago and has used a perception filter to disguise itself as part of Craig's house. The ship's emergency holographic program has been drawing in passersby, all who have a desire to escape, to find a replacement pilot for itself, but they were killed in the attempt. The machine identifies the Doctor as a possible pilot and tries to draw him to the controls, but the Doctor warns that if he should touch the controls, the ship could explode and take the solar system with it. The Doctor convinces Craig to touch the controls since he does not want to leave due to his love for Sophie, which will counteract the ship's protocols. Craig does so, and he and Sophie admit their love and share a kiss that breaks the ship's hold on the Doctor and themselves. The three escape in time to see the ship's perception filter wear off and implode, leaving Craig's undamaged one-story flat behind.
Craig and Sophie thank the Doctor, Craig giving him a spare set of keys in case he ever needs it. Aboard the TARDIS, the Doctor directs Amy to write the note that led him to Craig's house, using a red pen in his jacket; she rummages around and finds the engagement ring from her husband-to-be, Rory, whom she had forgotten after he was consumed by the crack in space and time and erased from existence.