The Eleventh Hour

The episode picks up from the ending of The End of Time. The Doctor has just regenerated and is crashing back towards Earth. After narrowly avoiding a collision with Big Ben, the badly-damaged TARDIS crash lands in the back garden of the young Amelia Pond in the small village of Leadworth. Amelia takes him inside and helps him satisfy his strange food cravings (only being satisfied with fish fingers and custard) before taking him upstairs to show him the crack in her bedroom wall. The Doctor discovers it is not just a crack in a wall, but a crack in time and space itself, and on the other side is a prison run by the Atraxi. The Atraxi deliver a warning to the two: “Prisoner Zero has escaped," but before the Doctor can help further he is interrupted by the TARDIS’s Cloister Bell: if not stabilised the engines will incinerate. The Doctor needs to pilot the TARDIS into the future to stop the engines from phasing. He promises Amelia he will return in five minutes, and leaves. She packs and begins to wait for him.

The Doctor returns but discovers that, for Amelia, twelve years have passed. Amelia, or Amy as she is now known, is working as a kissogram and uses her policewoman outfit to "arrest" the Doctor when he first returns to the house. He explains to her that the Prisoner Zero whom the Atraxi referred to has been living in Amy’s house by placing a perception filter on one of the rooms. Prisoner Zero - a serpent creature with the head of an anglerfish - takes on the form of a comatose patient, currently in the hospital where Amy’s boyfriend Rory Williams works, and chases the two out of the house after the Atraxi’s message from the beginning of the episode begins to play through every television, radio and electronic device in the world, adding that the "human residence" will be destroyed should Prisoner Zero not give itself up; the Doctor realises that they are referring to the entire planet.

The Doctor deduces that they have twenty minutes before the Atraxi weapons power up, and therefore only that amount of time to save the world. However, he is unable to access the TARDIS while it is rebuilding itself, and the Sonic Screwdriver is destroyed when he uses it to try and attract the Atraxi. He also discovers that Amy has been creating dolls and drawing pictures of him since his crash twelve years ago. With others who know her thus convinced of his identity, he uses a resident’s laptop and Rory’s phone to transmit a computer virus around the world that sets all clocks and electronic displays to the number zero, therefore notifying the Atraxi of Prisoner Zero’s presence and allowing them to track it to Leadworth as the source of the virus. He explains to Amy and Rory that the "Multiform," or Prisoner Zero, needs a dormant host and can change into the shape of whatever the host dreams of. Therefore, Prisoner Zero has eight disguises because of the eight comatose patients at the hospital. In a standoff in the coma ward of the hospital, the snakelike Prisoner attempts to steal Amy's dreams and memories to use as a disguise--manifesting as the Doctor and Amy's childhood self--but the Doctor prompts Amy to instead think of the undisguised Prisoner (which she saw earlier at the house); thus, Prisoner Zero manifests as itself, and is recaptured.

Although the Atraxi are now leaving, the Doctor calls them back and dons his new outfit to have a meeting with them on the hospital's roof. He tells them that aliens have invaded before and to look up how they were defeated. The Atraxi discover who the Doctor is and promptly leave. The Doctor then returns to the TARDIS, which by this point has finished repairing itself. He leaves to perform test runs and then returns to Amy, two years late. He shows Amy the regenerated TARDIS (complete with a new sonic screwdriver), and she agrees to travel with him on the condition he returns her home for the next day, which unbeknownst to the Doctor is her wedding day.