The Doctor and Martha runs into the TARDIS, and the Doctor makes sure that their pursuers didn't see her face. They dematerialize but the Doctor realizes they're being followed. He gives her a watch and tells her his life depends on it… and he wakes up from the dream. The Doctor gets out of bed and Martha comes in as a maid to bring him breakfast and addressing him as Dr. John Smith. The Doctor explains he sometimes has dreams of being an alien adventurer from another world, and she was with him. He notices the watch on the mantelpiece of his bedroom and claims he's from the Earth, but she shows him a paper showing he's in 1913 and he's completely human.
Dr. Smith is teaching at a boy's school in England while Martha works there and is treated poorly by the students. Dr. Smith runs into the school matron, Nurse Joan Redfern, and they chat about the boys. She wonders if he'll be going to the local village dance and he rather awkwardly falls down some stairs. Martha comes to check up on him but Nurse Redfern casually dismisses her as a maid who would have no medical knowledge. Dr. Smith talks about dreaming that he has two hearts but Redfern confirms he is a normal human with only one heart. He shows her his journal of his various dreams and the creatures he's seen such as Daleks, Cybermen, and the TARDIS. He also has picture of Rose, although she disappears from the later entries. Nurse Redfern leaves with the book and when Martha goes after her, she asks how Martha came to be there with the Doctor.
In the boys' dorm, Hutchinson tells one of the younger students, Tim Latimer to do his work for him. Latimer talks about Hutchinson's father's posting and seems to know what the letter says without having read it.
At the local pub, Martha discusses the suffragette movement with her fellow maid, Jenny, and talks about how she'll be free in a month. Martha notices a brief flash in the sky. Nearby, Nurse Redfern is walking home when she sees a green flash that probes the countryside. She runs to the pub where the Doctor emerges and dismisses her concern identifying it as meteorite, then offers to walk her home. Martha decides to investigate where the meteorite came down.
One of the boys, Jeremy Baines, is getting beer from where it's stored in the woods when the green object lands near him. He goes to investigate and runs into a barrier. Feeling around, he manages to find a doorway and enter it. Martha and Jenny arrive but it's too late: he's gone.
Inside what is a ship, unseen voices interrogate Baines and say he can't be allowed to leave. They then show themselves to him and he screams.
Back at the dormitory, Baines arrives and claims the beer is gone. Baines acts rather peculiar, sniffing the air, and Latimer senses something unusual.
The next morning, Martha rides to a nearby shed where the TARDIS is stored. Using the key, she goes inside and thinks back to how the Doctor warned their pursuers would never stop following them. He gave her a watch saying it contains "me," and says their life spans are running out so they only need to hide until they die. She remembers how the Doctor used a chameleon arch to rewrite his biology and transform himself into human. The TARDIS took care of everything else, creating a new identify for him. Martha then reviews a tape the Doctor left her of instructions to follow. She fast forwards to the point where the Doctor says in case of emergency she should open the watch.
Tim arrives to pick up a book from Dr. Smith, who wants to talk to him about his grades. While the Doctor looks for the book, Tim finds the watch and hears strange voices speaking of a "Time Lord." He briefly opens it and elsewhere on the grounds, Baines notices and reacts. Tim leaves with the book, and secretly takes the watch with him to his room where he opens it again. Baines returns to the school and then telepathically reports to his others, and they decide to "activate the soldiers."
Nearby, a landowner, Mr. Clark, is walking through the woods when he sees a scarecrow move. He checks it out but finds nothing inside. Then that scarecrow and others close in on him and kill him. A girl, Lucy Cartwright, is walking down the road with an umbrella when one of the scarecrows grabs her.
Dr. Smith is giving weaponry training to the boys when the Headmaster arrives. The other students blame Latimer for slacking off. Tim is haunted by a vision of the future and Hutchinson under attack. While Hutchinson takes Tim off for punishment, Baines seems to notice something odd about John Smith but dismisses it. Dr. Smith notices Nurse Redfern nearby and after she returns his book, he escorts her to the village where she talks about her fiancée who was killed. She talks about how in books he talks about a great war in the next year. He notices a piano about to fall on a woman and her baby and grabs a boy's ball to knock over pipes to set off a chain reaction that stops the woman from ending up beneath the falling piano. He then invites her to the dance, much to her obvious pleasure.
Dr. Smith and Nurse Redfern walk back to the school and notice a scarecrow. The Doctor adjusts it back on its post while he has vague memories of "Gallifrey." After they leave, the scarecrow comes to life and watches them go. Back at his room, the Doctor shows Redfern drawings he's made of her and he starts to kiss her. Martha comes in and finds them, then goes to the TARDIS and reviews the Doctor's instruction tapes but doesn't find anything to help and is clearly upset that the Doctor has fallen in love with someone other then her.
Tim is still examining the watch when he spots Baines meeting with Clark and Lucy, and they all start sniffing about the grounds. Meanwhile, Jenny is riding on the roads when the scarecrows capture her and take her back to the ship. Baines holds up a sphere claiming it is Mother of Mine and says she needs a shape. A cloudlike form emerges from the ship and enters Jenny.
Redfern is showing off her dress to Dr. Smith while Jenny arrives to see Martha. Jenny sniffs the air briefly and then asks Martha about where Dr. Smith will be leaving for. Jenny insists that Martha explain and Martha realizes something is going on and tricks her into revealing she's no longer human. Martha steps out and runs away and Jenny produces an alien gun and fires at her from the window but misses.
Martha runs to the Doctor and tries to explain, but realizes the watch is missing. She tries to snap him out of it, slapping him, but he dismisses her. Redfern mentions Dr. Smith did have a watch, which he can't remember. Outside, Martha runs back to the TARDIS, bumping into Tim who remembers her from the Doctor's past.
Baines and Jenny investigate Martha's quarters and realize it ties into Dr. Smith. They check things out and Clark shows up to show them a poster for the dance. They note that Lucy is already at the dance.
Redfern and Dr. Smith go to the dance and Tim follows them as they prepare to dance and Lucy watches. Martha comes in and confronts Redfern, pointing out that she must realize Dr. Smith is unusual. Then Martha apologizes and shows Dr. Smith his sonic screwdriver. She insists that he name it and he begins to realize things.
Baines, Clark, and Jenny arrive, killing a war veteran, while scarecrows surround the dance hall. Tim sees them and Clark and the others come in, killing anyone in their way. Martha tells Dr. Smith to remain silent, but they prepare to interrogate him and Lucy reveals he's the Doctor. Dr. Smith knows nothing about what's going on but Baines orders him to change back. They take Martha and Redfern hostage and Baines wonders what the Doctor has learned from being human. He then tells Dr. Smith to decide which one they will kill…