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An unusual episode that focuses on the Doctor (Amy being almost entirely absent) living as a human. He rents a flat (hence The Lodger) while investigating why the TARDIS can't materialise (trapping Amy in the future). There's humour, a love story, the Doctor playing football and another reference to the cracks.

The story begins with the TARDIS materialising. The Doctor steps out and is knocked over by a force. The TARDIS de-materialises with Amy on board, leaving the Doctor stranded. Using a note written by Amy, the Doctor heads for a flat and answers the ad for a lodger. He talks his way into renting it.

We meet Craig (the landlord) and his platonic friend Sophie. It is soon clear they are both in love with each other but neither has had the courage to speak up. A sub-plot is the Doctor, showing unusual awareness of the humans around him, realising this and helping them to find the courage to aim high in life and admit their feelings for each other.

We also see the Doctor inveigle his way into Craig's life. He cooks in the flat, he joins Craig's pub soccer team, wearing number 11 (for the 11th Doctor and episode 11) and stars in a victory over their opponents. (Actually Matt Smith seemed quite handy with the ball. Turns out he was aiming for a professional career before a back injury turned him towards acting.) The Doctor also sits in for Craig at his job (while Craig recovers from touching mould from upstairs) and does very well at it. In the end, Craig can stand it no more. The Doctor is being a better Craig than Craig. Jealous, he tells the Doctor to leave. The Doctor head-butts Craig (twice) to telepathically impart who is he is and what he's doing.

The mystery surrounds the floor above Craig's flat. What is up there that is luring people to their death, causing the mould and preventing the TARDIS from materialising. After Sophie is lured upstairs, the Doctor and Craig follow. The Doctor rescues Sophie as Craig and Sophie declare their love for each other. Upstairs is a time machine, hiding behind a (now ubiquitous) perception filter, looking for a pilot. It implodes as they flee.

The Doctor and Amy are re-united. The Doctor instructs Amy to write the note he received. She hunts through his jacket for a red pen and is startled to find her engagement ring (which she has no memory of). We see another crack in Craig's flat as they depart.