The Family wait for the Doctor to choose but Tim opens the watch, distracting them. Martha grabs the gun from Jenny and uses her as a hostage to force the others to let the civilians go. The Doctor and Joan get everyone out them but Tim runs away, saying the Doctor is as bad as the Family. Martha releases Jenny and tries to hold them off with her gun, but a scarecrow grabs her gun and she runs outside. she runs with Doctor Smith and Joan as Baines fires after them. Mother of Mine scans Jenny's memories and "remembers" Martha remembering a shack. Mr. Clark takes some scarecrow soldiers to investigate while the others follow Doctor Smith to the school.
At the school, Doctor Smith notifies the students who prepare their weaponry. Martha tries to convince Doctor Smith not to lead the students against them, and they have to explain to the headmaster that they're under attack. No one listens to Martha, who goes to find the watch. Tim still has it and is hiding, while Lucy enters the school to find it.
The headmaster goes out to confront Baines and Jenny, and Baines shows off his scarecrow soldiers. The Family demands Doctor Smith and Baines warns that he knows the future and war is coming in a year, and the school boys will die while using the headmaster's knowledge. Baines kills the headmaster's assistant and lets him go in to turn over Doctor Smith. The students rally, barricading the place, and Baines sends in his soldiers but Lucy warns the Doctor is preparing some trick.
Martha searches for the watch while trying to explain to Joan that the Doctor is an alien, but the matron doesn't believe her. Meanwhile, Clark lets the other Family know that he's found the TARDIS. Joan confronts the Doctor and tries to find out more about his background, but he doesn't know anything but the literal facts. She notes that the Doctor John Smith she knew wouldn't want the boys to fight, and he kisses her before going to join the battle.
Hutchinson prepares for war with Tim, who reveals he's seen he future where they fight together in the war to come. Tim runs off, believing he was given the watch to help, but Lucy spots him. He shows her some of the memories of the Doctor from the watch and she runs off in terror. Baines and the others, knowing what she knows, orders the attack and the schoolboys open fire, destroying the first wave of scarecrows. Doctor Smith looks on, holding a gun, but can't bring himself to fire. They realize the soldiers are nothing but straw, and then Lucy comes in. Martha tries to warn him but he ignores her and Lucy kills him. Doctor Smith orders the boys to retreat rather than risk more death, and they flee into the school while the scarecrows close in. They get some of the boys out to safety while searching the others for the watch. They prepare to shoot the boys but Tim opens the watch, drawing them upstairs while he escapes.
Doctor Smith, Martha, and Joan run out into the woods but the Family have brought the TARDIS and call out, telling him to come back. Doctor Smith doesn't recognize it even though Joan points out he wrote about it in his dream journal. In a near panic, Doctor Smith insists on being John Smith and Joan takes them into the village to hide at an empty cottage where Lucy's parents lived. Meanwhile, the Family goes to their ship and prepares to attack.
Tim comes to the cottage to bring Doctor Smith the watch. John refuses to take the watch but they're interrupted as the Family begin to bombard the village. Doctor Smith takes the watch and starts to recover his memories, but is furious that "he" will have to die for the Doctor to return. He suggests giving the watch to the Family, but Joan reads his dream journal and reveals the Family would live together and spread destruction. She asks Martha to leave her and John alone, and then explains he must revert back. Doctor Smith sees a brief vision of what his life would be like if he remains human, marrying, having children, and dying of old age.
Doctor Smith goes to the ship and asks them to stop the bombardment, and they do after determining he's still human. He offers them the watch and they take it after casting him aside, but open the watch to find it empty. Doctor John Smith stands up and reveals that he is… the Doctor, having fooled their olfactory senses. The Doctor has rigged the controls to destroy the ship and they all run out as it blows up.
Baines is left to describe what the Doctor did to them afterwards: binding Father of Mine in dwarf star chains, Mother of Mine in a black hole, Sister of Mine in every mirrors, and Brother of Mine trapped as a scarecrow.
Having given each of the Family the immortality they wanted, the Doctor returns to see Joan. She notes that Doctor Smith was willing to die for him, and he asks her to join him in his travels. She refuses and asks if any of the death and devastation would have happened if he hadn't come there on a whim. The Doctor doesn't have an answer, and turns and goes. Joan is left with John Smith's book of dreams.
The Doctor returns to the TARDIS where Martha is waiting for him, and says it's time to move on. Martha denies having any feelings for him and he thanks her for looking after him. Tim says goodbye and thanks him for seeing the future, and is resolved to fight in the wall. The Doctor gives him the watch as a good luck charm before they leave in the TARDIS.
Years later, the Doctor speaks of World War I and how Tim uses the Doctor's watch to determine when the artillery will hit, letting him save himself and Hutchinson. The two men make it to safety… and many years later Tim is at a memorial for the war while the Doctor and Martha, unchanged, look on.