The Doctor and Martha run into the TARDIS as someone opens fire on them. The Doctor quickly determines that their pursuers didn’t’ see either one of them, then dematerializes the ship. However, he warns that their pursuers have time travel technology and won’t stop until they catch them. He gives a watch to Martha and… wakes up from a dream. He’s Dr. John Smith, a teacher of history at boy’s school in 1913 in England. Martha is his maid, who reassures him that he isn’t from the future and isn’t an alien adventurer.
Dr. Smith goes to the school to teach and runs into Nurse Joan Redfern, the school matron. They chat while the boys, led by Hutchinson, taunt Martha as a member of an inferior race. When Dr. Smith accidentally falls down some stairs, Martha goes to check up on him but Nurse Redfern casually dismisses her as simply a maid. Dr. Smith starts talking about his dreams and shows Joan a book that he has written of them, featuring sketches of such creatures as Daleks and Cybermen. Redfern leaves with the book and Martha tries to get it back without any success.
In the boy’s dormitory, Tim Latimer is forced to do chores for the older boys like Hutchinson. However, Tim displays the ability to know where Hutchinson’s father has been posted without reading his letters, which makes Hutchinson suspicious. Tim hastily tries to explain that he sometimes gets odd hunches about little things. Hutchinson shrugs it off and sends another boy, Baines, to get some beer they hid in the nearby woods.
At the local pub, Martha discusses the suffragette movement with her fellow maid Jenny when they see a brief flash in the sky. Nurse Redfern, walking to the pub to meet the Doctor, sees a strange green beam sweep over the countryside. She runs to the pub where the Doctor is waiting. He says all they saw were meteorites and offers to walk Joan home. Baines sees the same flash and goes to investigate, and finds an invisible ship. He manages to get inside just as Martha and Jenny come to investigate and see nothing. Inside the ship, strange voices talk to Baines and say he can’t be allowed to leave. As they reveal themselves, he screams in terror. Later “Baines” returns to the boy’s dormitory and acts strangely: he’s clearly possessed by some alien force.
The next morning Martha goes to a shed where the TARDIS is hidden. She goes inside while remembering how the Doctor figured out that their pursuers had a limited lifespan and wanted him as a Time Lord, so he used a chameleon arch to transform himself into a human. He stored his essence in a watch and told her to open it only in emergency, as their trackers would be able to lock onto it and find them.
Tim arrives to get a book from Dr. Smith and notices the watch. It seems to talk to him about Time Lords and when he opens it up, Baines senses something. Tim closes it then secretly takes it with him after Dr. Smith gives him his book. He takes it back to the dormitory and opens it again. Sensing the trace, Baines contacts the other members of his “Family” and tells them to activate the soldiers.
In a nearby field, Mr. Clark a landowner notices a moving scarecrow. Thinking it’s a prank, he checks it out but there’s no one inside. It then comes to life while other surround and capture him. Nearby, a young girl, Lucy, is walking down a road with a balloon. A scarecrow captures her and takes her back to the invisible ship.
Dr. Smith is assisting with weapon training and Tim isn’t doing too well, as he objects to firing on natives armed with spears. Dr. Smith lets Hutchinson punish Tim while Baines looks on, suspicious. Dr. Smith then walks Nurse Redfern to the village where he notices a piano about to fall on a woman and her baby. He manages to use a ball to knock over some pipes and stop her from being crushed by the piano, much to Redfern’s surprise and pleasure. He invites her to a local dance and they walk back to the school, noting a seemingly harmless scarecrow along the way. Back in his rooms, he shows Nurse Redfern drawings he’s made of her and then they kiss. Martha comes in and sees them and is clearly upset that the Doctor has fallen in love… with someone else.
Clark and Lucy arrive on the school grounds and meet with Baines. Tim notices them while examining the watch and makes sure they don’t spot him. Jenny is riding back when the scarecrows capture her and take her to the ship. Baines is there with the others and produces a green sphere. Announcing that “Mother of Mine” will use Jenny’s body, he unleashes a green sphere which possesses the maid’s body.
“Jenny” then goes back to the school and starts asking Martha questions about Dr. Smith. Realizing something is wrong, Martha slips out and manages to escape after Jenny fires an alien weapon at her. She goes to the Doctor and tries to snap him out of it, slapping him, but he dismisses her as insubordinate. Martha runs back to the TARDIS, bumping into Tim who “remembers” her from the memories inside the watch.
Redfern and Dr. Smith go to the village dance, unaware that Lucy and Tim are watching them. Baines and the other two figure out that Dr. Smith is at the dance and go there with their scarecrow soldiers. Meanwhile, Martha goes there and tries to convince Nurse Redfern that something is wrong. Redfern realizes that there is something hidden about Dr. Smith, and when he comes over Martha tries to get him to acknowledge his sonic screwdriver. Before he can remember anything, the “Family” arrives and takes everyone prisoner. Baines demands that the Doctor change himself back to a Time Lord, as he is useless to them as a human. When he tries to explain that he can’t, and doesn’t know what they’re talking about, they give him a choice: they’ll kill Martha or Redfern if he doesn’t change himself back, and he gets to choose which one dies…