Vicky Caine has been babysitting. As she leaves the house and makes her way up to the bus stop she realises that her watch has stopped and that she may have missed her bus. It is a chilly October night and after waiting for a while at the stop she becomes sure that the last bus has already gone. Faced with the dilemma of returning to the house where she babysat and asking for a lift home or taking a taxi, she opts for the latter. Sadly, her phone has no signal so she decides to walk home. The problem is that the road bends so far away from her intended direction due to the huge loop it makes to bypass the woods. In the distance, the town hall clock chimes half past ten and she knows that she is going to be in trouble when she gets home. She decides to leave the road and skirt round the edge of the woods to save time. The idea of the woods scares her, as it does everyone in Foxton. For generations people have stayed away from Swallow Woods. Vicky decides that, as nobody local will go close to the woods, it must be safe to walk nearby. She hops over a fence and crosses the field that borders the woods. However, she slips on some mud and tumbles through the darkness into the edge of the trees. She tries to walk away from them but it seems she is going further in. her passage is watched by a fox, the last creature to see her for some time.

The pubs close at nine thirty in England during the First World War. Emily Bostock, the barmaid at the Fox has been aware of the young man in the corner watching her. She is irritated when the obviously fit and healthy man is presented with the white feather of cowardice by one of the regulars and speaks out in his defence, pointing out that none of them have been laying down their lives for their country. She tells the young man that he can walk her home if he likes. As they step out onto the lamplit street he tells her his name is Rory Williams. He points out that he doesn't know where she lives. She nods at the darkness of the countryside and says that it is four miles away. This doesn't seem to trouble him and they link arms.

As they walk she expresses surprise that the white feather didn't bother him. When he says he didn't understand what it was at the time she suspects that it may be that he is a spy or a conchie. He tells her that he doesn't know what a conchie is: his explanation that he has been away travelling barely satisfies her but she gives him the benefit of the doubt. She decides that having an escort should make it safe to take a short cut near to the woods. When they find themselves unexpectedly near the trees she says she doesn't believe in the legends about Swallow Woods swallowing people. Rory is perplexed when he can hear the distant sound of a motorway but Emily doesn't seem to notice it. She is feeling slightly foolish, being in the dark with a man she barely knows, and worries what the locals will say about her. On an impulse she runs into the trees, daring Rory to catch her. He follows and they are not heard of for quite some time.

Four days after the disappearance of Vicky Caine, the Doctor is being held by the local police on suspicion of abduction. He finds himself in an interview room with a broken clock and a broken blind. Two detectives enter: a red haired man and a blonde woman. The Doctor tells them that he is running short of time. They question him about a woman called Laura Brown who has disappeared recently. He denies meeting her and adds that he never met Vicky either. As neither of them have mentioned Vicky this only implicates him further. He tells them that they don't understand the situation and that only by releasing him can he resolve it. This, naturally, cuts no ice.

Two hours later, in front of the police station, the male policeman, Galloway, announces that a young man in his mid twenties is helping the police with their inquiries into the disappearances of Laura Brown and Vicky Caine. The assembled media ask if it is now a murder investigation and if the local woods have been searched. A local reporter, Jess Ashcroft, working for the Herald, chats to one of the television journalists. They flirt mildly and arrange to go for a drink later. Jess is pleased because Charlie is both handsome and a contact with the national news media where she sees her future. Before she can go to join Charlie for a drink, Jess is accosted by a woman who introduces herself as Amy Pond and warns her that Jess will be the next person to disappear.

The TARDIs lands in Long Lane, just outside Foxton. The Doctor, Amy and Rory emerge into the chilly October air. The Doctor tells Rory to spend the afternoon in the Fox and get to know Emily Bostock. He gives Rory a small triangular device and tells him to press a button on it when he gets to wherever he is going with her. He says that the TARDIS will be there in a flash. He adds that there is something in the woods that might disorientate him so concentration is vital. As the TARDIS dematerializes, taking the Doctor and Amy with it, Rory starts walking into town.

Detective Inspector Gordon Galloway reflects on how he met his wife on holiday and ended up transferring to her home town where he has lived for eighteen months. It isn't the mysterious disappearances of Laura and Vicky that make him feel uneasy: the town itself seems strange and insular as if it were hiding a secret. The idea that he had arrested a suspect seemed alien to both sets of parents. In addition, he had tried to instigate a search of the most likely place for the girls - Swallow Woods - and yet it simply hadn't happened. People were always too busy, or equipment was broken. Worse, there was his chief suspect. When he asked DC Ruby Porter if it was the right man she agreed that she thought it was but when pressed to explain all she could say was that he seemed both young and very old at the same time.

Galloway and Porter return to the interview room. When they do, the Doctor grabs Galloway's wrist and stares intently at his wrist. He stares at Galloway intently and tells him, 'Amy and Jess. It's time.'

Jess tries to meet Charlie in the Fancy Fox pub in town but is intercepted by Amy who drags her to a separate table. Amy tells her urgently that she knows all about the woods. She produces a plastic bag and empties the contents onto the table. She extracts a series of aerial photographs of the woods and hands them to Jess. The first shows the motorway and how it swings away to pass around the woods. Another photograph, taken much earlier, shows the road following the same track when the village was much smaller. Amy hands her a third photograph and says that it is the Roman road and it follows the same route. Finally she shows her a photograph from before the time of roads, showing a footpath curving away from the woods. Amy says the photograph was taken earlier in the week, or six thousand years ago. She goes on to say that since the Bronze Age people have been avoiding the woods and yet, every fifty or so years, people have been disappearing into the woods and never coming out again. She shows some other documents, from the Domesday Book and from Parish records that not only indicate these mysterious disappearances but also prove that nobody owns, or wants to own, Swallow Woods. Finally she hands Jess a newspaper, dated the following day, which names Jess Ashcroft as the third girl to go missing. Amy tells her that as far as she is concerned, Jess has already gone. But, this time, Amy is going with her.

Rory blunders through the trees looking for Emily. She pelts him with a pine cone from a perch up a tree. She tells him there is nothing to fear in the woods but he points out that night has already turned to day in the woods and autumn has become summer. He tells her that there is a broken time engine in the woods, making strange things happen. Emily takes this in her stride and asks if she can help him locate and dispose of the engine. He doesn't tell her that, according to history, Emily is never heard of again after that night.

On the TARDIS, the Doctor tells Amy about the damaged warp drive of the craft in the woods and how it creates temporal and spatial anomalies in the wood which cause people to go missing.

After an hour of walking, Emily and Rory find a glade in the trees. The glade is still and huge, reminding them of a cathedral. At its centre is a pool and, beside it, the remains of a campfire. Emily suspects it belongs to Harry, a young man who ran away to avoid conscription into the army. Emily makes a romantic pass at Rory he blurts out that he is married. Mortified, she turns and runs into the trees. Rory turns to follow but he feels dizzy and faint.

Amy shows Jess one last aerial photograph. She says it was taken fifty years in the future and shows a lake where the woods should be and countryside instead of the town. Amy tells her that she doesn't know how it happens but the obliteration of Foxton occurs in the next few days. Jess is sure that the photographs are fakes but Amy asks why she would do such a thing. Instead she questions why nobody in the town will approach the woods and yet, at fifty year intervals, somebody is drawn to enter. Charlie comes over to offer Jess a drink but she makes an excuse, saying she has to cover a pensioner's birthday party, so he gives her his number. Then she tells Amy that they need to be going.

When Rory wakes up, he realises at once that he is breathing the recycled air of an alien space ship but he can see an October wood. He can also hear the throb of the ship's engines. Emily comes to help him to his feet but he cannot remember either his own or her name. She reminds him of both while he discovers that they are in a small hold and the walls are metallic but patterned to look like woodland. He tells her that, apart from her running off, he can remember nothing. She tells him that they are looking for a damaged engine so he follows her through a doorway. In his pocket is a triangular device but he has no idea what it is for.

Amy and Jess park in Long Lane near the woods. Amy tells Jess about how she and the Doctor left Rory in 1917 and then how he never sent the signal they were expecting. Amy was supposed to follow Laura into the woods but the signal still didn't come, nor did it before Vicky vanished. That was when they popped into the future and found that Foxton was gone and Jess was the last person to disappear. Thus Jess is their last chance to save the town. Jess says that she had noticed the Doctor around town and had been trailing him which exasperates Amy because it explains why she had such a hard time catching up with Jess. They leave the car and enter the woods.

They step out of the October night into a forest on a summer day. As they pass through the trees the seasons change. They enter a glade in winter and find a brooch in the shape of a butterfly. It seems to have been there forever. Then they encounter Vicky Caine.

Rory and Emily are discussing whether the ship is in flight. He is surprised at how knowledgeable she is about future science but she tells him that she read H.G. Wells stories with her fiancé, Sam, before he was killed in the war. She tells Rory that he'd said the engines on the ship were dead but from what she has seen the ship seems very much alive.

When Galloway returns to the interview room he finds that the Doctor has repaired the blind and dismantled the clock. Galloway wants to know how the Doctor knew that Jess would disappear: her car has been found near the woods. Instead the Doctor orders him to be silent and listen. Galloway can hear nothing but Porter can. The Doctor surmises that she has lived in Foxton all of her life and is used to the sound that he has only just hear: the space ship's propulsion unit is still operational. That means there must still be somebody on the ship maintaining it: the pilot is still alive.

Vicky tells Amy and Jess about how she ended up in the woods and arrived at the glade. She says that no matter which way she walked out of the glade she always returned to it and as she went round in circles the seasons changed. She also saw someone with reddish, brownish hair who might have been a man. This person tried to get her to follow him into the wood but she had chosen not to. Just as Amy is debating on their next course of action she sees a fox enter the glade. The fox transforms into a man with reddish, brownish hair and beckons to her. Immediately, Amy tells the other two to try to find a way out of the woods while she follows the man.

Rory agrees that the ship seems to be alive. They enter a room with a large, flat console. Emily waves her hand at it and images appear on the surface, scrolling rapidly. She manages to slow the text down so that they can discern pictures of humans. One of them is Harry Thompson who has been missing for six weeks. Others seem to be in historical clothes dating back through the ages. Then they hear footsteps approaching and Rory tells Emily to run.

Amy follows the fox-man out of the trees to a beautiful landscape of rolling countryside with a fairytale castle at the centre. Amy tells him she is too tired to make the journey without a rest. The fox-man waves his hand and the distance collapses until they are at the gate. A white haired woman approaches and welcomes Amy. She introduces herself as Laura Brown.

Galloway has finally got his men to erect searchlights near Swallow Woods. The rain is pouring but Galloway suspects that this is not the only reason why he has no local officers among his men: everyone around him has been drafted in from elsewhere. Before he can enter the wood, Galloway sees two figures emerge: Vicky and Jess. The paramedics try to lead them away but Jess demands that Galloway release the Doctor. She says a storm is coming and the Doctor is the only one who can stop it. Jess explains the time distortions and spatial pockets to Galloway but he merely thinks that it is a prank thought up by Amy. Ruby Porter joins Galloway for the interview and is less disbelieving. As soon as Galloway leaves to resume the search of the woods Jess appeals to Ruby to talk to the Doctor.

Rory and Emily have nowhere left to hide after running through the ship. All of the passages lead back to the control room and it is there that they are found by a young man. Emily recognises him as Harry Thompson but it is obvious to Rory that Harry has been taken over by someone else.

The were-fox is called Reyn: he and Laura seem to be very close friends, reminding Amy of an elderly couple. Laura explains that only ten days have passed in the world outside but she has been in the woods for almost sixty-one years. She insists that she is not a captive and, as the trio settle down to a meal, she helps Reyn tell his story. He recounts how his ship crashed centuries earlier and that he had no way of repairing it. The ships used by his people were unusual in that they learned from their travels and eventually came to consciousness in a process called The Shift. The ship in the woods has been taking people every fifty years or so and learned from their experiences. Reyn says he tried to stop them entering the ship by luring them to his home but he has not always been successful. Amy asks whether Rory has passed this way but Reyn says that he must have gone into the ship. She then asks why he doesn't let the Shift finish and allow the ship to leave but Reyn says that such a thing could be disastrous. With the time and space pockets that the ship has created any departure could have untold consequences. Amy replies that within a week something is going to happen that will turn the woods into a lake. She refuses to say how she knows this. Reyn says that if people tried to get out of the ship such a crisis might happen.

Ruby Porter slips into the cells of the police station. She finds the Doctor and demands to know what is happening. He replies that it is all aliens and space ships. He seems to be optimistic until he hears that Jess and Vicky escaped the woods without Amy. Porter tells him that her uncle was lost in the woods when he was fifteen, back in 1959. He tells her that he can end this situation and all the disappearances. She agrees to let him help.

Although Amy can see a large chamber around her and Reyn and Laura, she feels as if she is trapped in a small space. She knows that the medieval hall is an illusion. Laura tells her that it has been a variety of things in her time: a space station, a gothic mansion, an intergalactic empire. Amy replies that she has been trapped five miles from home and never actually been anywhere. She says that she is not going to submit like Laura but is going to find a way out. Reyn permits her to leave but says that she will soon be back.

Emily soothes Harry, ignoring Rory's assertion that the young man has become something else. From things Harry is saying, Rory pieces together details of a flight through space and then arrival on Earth followed by learning from 173 people. He realises that the ship steals memories and that is why he can't remember who he is. Emily wonders how a man can be a ship. Rory berates the ship/Harry for what it has done. Harry replies that he is sorry to be born. As he does so the lights flicker and a great gale blows through the woods.

At the door of the police station, Jess is waiting for a car to take her home when she sees Porter giving the Doctor his screwdriver and leading him out into the rain. Jess joins them as they enter Porter's car.

Amy finds herself running in circles through the woods. The trees are lashed by the wind, rain pours in and the ground is full of water. Reyn watches her, telling her that there is no way to leave. He is promptly contradicted by the Doctor.

Amy runs over, demanding to know where the Doctor has been. He tells her he has broken out of jail but she assumes this means they let him out. He tells her that Jess and Vicky escaped the woods and then looks around him. Amy introduces him to Reyn. The Doctor says he recognises the species and talks about the Long War before abruptly breaking off. He asks how the ship came to crash and Reyn recounts an attack by enemy gunships and his decision to hide out on Earth. He adds that the Shift began while he was first encountering people. Amy interrupts to find out about the Long War. The Doctor tells her it was a territorial conflict between neighbouring empires. Reyn adds that it has been going for generations. The Doctor says he will help to guide the ship through the Shift and maintain the integrity of the environment. In the distance, dogs can be heard approaching. Around them the trees seem to be in chaos: some are autumnal, others are in full leaf or bare. Reyn promises to lead them to the ship as well as he can. The Doctor tells him to lead the dogs astray while he and Amy look for the ship. As they do so the Doctor tells Amy not to trust Reyn. He adds that the Long War has been finished for a long time and the ending wasn't happy.

The Doctor leaves Amy and Reyn to return to Laura while he makes his way into the ship. Rory doesn't recognise him but Emily fills him in on details about Harry's desertion and the ship's guilt at the people it abducted. The Doctor remarks that this is a lethal combination of shame and guilt but Rory and Emily manage to talk the ship out of its suicidal impulse and the Shift is complete. In his control room Reyn is listening to all of this with Amy and Laura. He produces a weapon and promptly orders the ship to return to the War.

Emily shouts back that there is not going to be a war. The Doctor suggests that they ask the ship what it wants to do but Reyn says the ship has a duty. Despite this the ship refuses to re-enter the war. This prompts Reyn to materialise beside them, along with Laura and Amy. Reyn says he shall execute the ship and then fly its shell anyway. The Doctor is appalled; the effects of killing the ship would be detrimental to anyone who had contact with it in unimaginable ways. Even Laura pleads with him to rethink. The Doctor tells Rory and Amy to press the buttons on the triangles he gave them earlier and the TARDIS promptly materialises beside them. The Doctor tells Reyn to leave the ship alone and in return he will use the TARDIS to take him home. Reyn realises that this is the right thing to do and lowers his gun.

Reyn and Rory travel with the Doctor but when they reach their destination Reyn barely recognises his planet: underground tunnels and turrets spiking the clouds are the landscape. The Doctor tells Reyn that the war is long over and nobody won. His people are more mistrustful and have all but forgotten the Long War other than in myths. However, he says that Reyn is a legendary figure of hope who will bring back the technology (since forgotten) to teach ships how to live again. Reyn is appalled and asks to be taken home to his ship but a child spots him at the TARDIS door and recognises him as the Traveller. A crowd gathers and welcomes Reyn, carrying him like a hero.

The Doctor and Rory make a trip back in time to leave the seeds of a story about a traveller returning from the past, emerging from a blue box with forgotten knowledge.

Back in the ship the Doctor tells Laura it is her turn now. She understands that she has to seal up the ship and close time around her. The Doctor says that it is safe for the ship to leave and Laura can go with it to visit the universe for real. Emily and Harry (now returned to his prior self) agree to go with her.

Amy and Rory watch the TARDIS screen as the ship leaves the woods and Rory pins Emily's butterfly brooch to Amy's lapel. The Doctor opens the door and they look down on Swallow Woods. Like a speeded up film they see people come and go through the woods. Only Emily and Harry and Laura will be counted among the mysteriously vanished - everyone else who went into the woods throughout history has been saved.

Galloway awakes from a nightmare about being trapped in a forest in a storm to find the phone ringing: Laura calls to tell him that she is safe and has gone on a gap year without telling anybody. Later, his wife tells him they should leave Foxton and move north. Vicky Caine and all of the other disappeared have their lives back with no memory of entering the woods (stretching back to the Bronze Age). Ruby Porter never even became a police woman, lecturing in history instead.