In France, 1890, Vincent van Gogh writhes in his bed, calling out while the doctor at his side and Madam Vernet comment on one of his paintings. Apparently it is worse than usual.

In the Cabinet War Rooms, 1941, Professor Bracewell shows Winston Churchill a Van Gogh original and tells the Prime Minister to get a message to the Doctor.

In the Stormcage Containment Facility, 5145, a prison guard on his first day of duty answers the phone. River Song hears the Doctor's name mentioned and demands to have the phone. It is Churchill, telling her about Van Gogh's painting. The guard takes the phone and River kisses him. He is aware that she has tried to use her hallucinogenic lipstick and holds her at gunpoint. Unfortunately for him, he is pointing his gun at a drawing on the wall: she has escaped.

In The Royal Collection, 5145, River Song steals a painting. On her way out she is confronted by a gun-toting Queen Liz 10. River tells her she needs to get the painting to the Doctor.

In the Maldovarium, 5145, River is buying a vortex manipulator from Dorium Maldovar. She pays for it with a Callisto Pulse (capable of deactivating micro-explosives from up to 20 feet - just like the ones she has placed in Dorium's drink).

The Doctor has decided to go to the oldest planet in the Universe, Planet One. The cliff faces are made of pure diamond and contain an otherwise indecipherable inscription. The TARDIS translates it as "HELLO SWEETIE". There are time-space coordinates beneath the message.

The TARDIS lands in Roman Britain during the 2nd century AD. The Doctor is greeted by a Roman soldier who thinks that he is Caesar. Amy says that the Romans were her favourite topic at school. The soldier takes them to Cleopatra (or, rather, River Song in disguise). She shows them the painting; a picture of an exploding TARDIS.

Rivers tells the Doctor that the title is 'The Pandorica Opens'. Amy wonders what a Pandorica is: River tells her it is a prison for the most feared thing in the Universe while the Doctor contradicts her and says that it is a myth or a fairy tale. He consults a map, saying that if somebody had hidden such a device they would want to remember where they left it.

They gallop across the plains on horseback, arriving at Stonehenge. The Doctor uses his sonic screwdriver to find a way beneath the monument into the Underhenge. They fail to see a severed head of a Cyberman lying behind a rock but at the bottom of the steps the Doctor glances at a Cyberman's arm lying on the floor. He uses his screwdriver to light flaming torches.

The Pandorica is a large metal cube. He recounts the fairy tale that says a warrior or goblin, feared by the Universe, capable of arriving on a planet and changing life there forever, was trapped inside by a good wizard. River says that the Pandorica contains many levels of security; locks, time codes and matter lines. Each is being opened, one by one. The Pandorica will open in a few hours. The Doctor wonders who is inside and whether they have met before. Amy asks how Vincent van Gogh could know about it when he isn't due to be born for centuries. She comments on how similar its name is to Pandora's Box, her favourite childhood story.

River and the Doctor say that the stones around them are transmitters, broadcasting to the Universe. They wonder who else knows that the Pandorica is opening. A quick scan tells her that at least ten thousand ships are in orbit: a Dalek saucer, a Cyber Ship, Sontarans, Slitheen, Drahvin, Chelonian and Atraxi among them.

The Doctor decides the Romans are the greatest military machine in the history of the universe and sends River back to them to get help. Unfortunately, news has arrived from Egypt that Cleopatra is dead. River tries to use her disintegrator pistol to demonstrate her power. Before the Roman commander can answer, a volunteer arrives; Rory Williams dressed as a Roman soldier.

In the Underhenge, Amy produces the engagement ring that she found and asks the Doctor if he is planning on proposing to someone. He tells her it is a memory of a friend who was lost. While something stirs in Amy's mind he asks her if it bothers her that her life doesn't make any sense: there are too many rooms for a start. Just then, the arm of the Cyberman reanimates and its gun starts to shoot randomly. The Doctor grabs it but it electrocutes him and it passes out. The head crawls in, using wires as tentacles, and attacks Amy. She fights it off but it fires a dart into her neck. As she begins to feel woozy, the body of the Cyberman lurches in. Amy hides behind a door with the Cyberman trying to break in. Rory arrives and kills the Cyberman with his sword and Amy passes out.

The Doctor wakes up and eventually realises that one of the soldiers is Rory, who tells him that he died and woke up Roman. The chamber shakes as space ships close in from above. The Pandorica is in the final phase of its opening. River calls to tell the Doctor that the sky is full of ships. He tells her to bring the TARDIS: there is equipment in it that he needs. He goes back to the surface and steps onto a stone. From there he addresses the fleets in the sky above him, telling them that he has the Pandorica and challenging them to come and take it from him. The ships move off to argue - so he thinks - about who should try to take it first.

The Doctor warns Rory that something bad is about to happen: Amy wakes and does not recognise her fiancé. She goes to get some fresh air while Rory tells the Doctor that he died and woke up there with a head full of Roman things. The Doctor throws him the engagement ring and tells him to go after Amy.

River tries to take the TARDIS to Stonehenge but it malfunctions and then transports her to Leadworth, on 26th June 2010. She exits, wondering why it has brought her here. After she has gone, the scanner screen cracks and a voice intones "Silence will fall". As River enters the darkened house she notices the scorch marks on the ground and a broken front door. In Amy's bedroom she finds a book on Roman Britain which contains an illustration of the Roman commander she has just left. Beside it is a book about Pandora's Box. She tells the Doctor this and they guess that somebody has been in Amy's subconscious to create a plausible scenario as a trap for him. He guesses that the Romans don't even realise that they aren't real.

She returns to the TARDIS but it seems somebody else is flying the TARDIS. She phones the Doctor and he tells her to shut off the engine but she can't. He asks her the date and she tells him 26th June 2010. He implores her to land the TARDIS and get out before it explodes. When she tries to leave she finds that the doors are locked.

The Romans are triggered by a high-pitched sound and their hands drop to reveal guns; they are Autons, under the control of the Nestene Consciousness. The Doctor is led to the Pandorica where the Dalek Supreme is waiting with an Eternal and a Drone. They tell him that the Doctor is responsible for the end of the universe and a Cyber Leader concurs. Other aliens arrive and the Doctor realises they have formed an alliance. He clings to the hope that they have come for his help but he is fixed into a seat in the Pandorica as they tell him their alliance is to save the universe from him.

Amy remembers who Rory is but he is fighting to master the Auton commands. He tells her to run but she says she will never leave him. Against his will, he shoots her and she dies in his arms.

The Doctor tries to tell his captors that the TARDIS is the cause of the explosion and he is not aboard it. The Daleks insist that he is the only person who can fly it. He tells them that there will be a total event collapse: every sun will supernova, at every moment in history and the universe will never have existed. River finally opens the TARDIS door but in it opens onto a stone wall. She says that she is sorry as the TARDIS console explodes. Stars explode across the galaxy and only the Earth remains.

It is 1996 and Amelia Pond is praying by her bedside for help with the crack in her wall. Nothing happens.

She has drawn a picture of the Moon and stars. A psychiatrist and Amelia's aunt explain to her that there are no stars in the sky: there is only the moon. Amy sits on the stairs, eavesdropping on their conversation, when somebody drops a pamphlet for the National Museum through the letterbox. Amelia picks it up and sees a note telling her to visit. Her Aunt Sharon takes her to the Gallery. Amelia goes to the Pandorica and finds another note saying "Stick around, Pond". Her drink is abruptly stolen from her.

The museum closes: Amelia has hidden and is still inside after everybody else has left. She returns to the Pandorica and touches it. The cube lights up and the Pandorica opens. Inside is Amy Pond, telling her that "This is where it gets complicated".

Back in 102 A.D. Rory is cradling the corpse of Amy. The Doctor appears, using a vortex manipulator. He tells Rory that Amy isn't dead before contradicting himself, adding that it isn't the end of the world (and then contradicts himself again). He tells Rory to rescue him from the Pandorica and gives him the sonic screwdriver, asking him to put it in Amy's top pocket when he has finished. Rory opens the Pandorica and lets the Doctor out. The Doctor and Rory take Amy down into the Underhenge where they find stone statues of the Daleks, Romans and Cybermen. The Doctor says that they are fossils of the Universe. They put Amy into the Pandorica while the Doctor explains that it is designed to be so secure that death is not an escape. He says that the cube will heal Amy when it is touched by her DNA in two thousand years away. He leaves a telepathic message in Amy's head so that she will know what is happening when she wakes up and then prepares to jump back to the future but Rory chooses to stay and guard Amy in the Pandorica. The Doctor tells him that he needs to avoid heat and radio waves and to stay out of trouble.

Amy looks at one of the museum's video exhibits that tells the story of a Roman centurion that followed the Pandorica through its two thousand year history, protecting it against any dangers. He was last seen in 1941 when a fire threatened it and he dragged it to safety. Amy recognises the centurion as Rory.

A stone Dalek comes back to life and says "Exterminate." The Doctor re-appears as the Dalek comments that its weapons systems are restoring. A security guard, Rory, shines his torch on the Dalek and then shoots it with his Auton hand-gun. The Dalek's vision is impaired and the four of them run. The Doctor has acquired a fez and is carrying a mop. Rory says that this is how he looked when he gave him the sonic screwdriver all those years ago so the Doctor takes this as his cue to leap back in time. After setting up his rescue from the Pandorica he also drops off the pamphlet at Amelia's house and steals her drink from earlier in the day (because she has just told him she is thirsty).

Another version of the Doctor appears at the top of some steps. His clothes are smoking and he tumbles to the floor, unconscious. As the Doctor scans him the unconscious Doctor revives and whispers something in his ear and then apparently dies. The Doctor says he has twelve minutes to live. Amelia has disappeared and the Doctor says that the universe is still collapsing and they are only temporary anomalies. The Dalek starts restoring itself as the three of them make for the roof.

The Doctor shows them the Sun. He asks them what it can be if every other star in the universe has been wiped out of existence. With the aid of a satellite dish and his sonic he proves that it is the exploding TARDIS. He also picks up the sound of River, caught in a temporal loop created by the TARDIS to protect her. She is saying "I'm sorry my love." The Doctor uses the vortex manipulator to collect her and fetch her back to the roof. Her first reaction is to take the Doctor's fez and obliterate it with her pistol but the stone Dalek immediately appears, hovering above the parapet. They escape down into the building. The Doctor tells them that the light from the Pandorica is a restorative field which re-activated the Stone Dalek .The Dalek had been only an echo in time but the energy brought it back into existence. The Doctor says he intends to use the Pandorica to reboot the Universe.

The Dalek follows them and shoots the Doctor and, as he falls, he uses the vortex manipulator to jump back into the past. River makes the Dalek beg for mercy before killing it. Amy and Rory return to the stairs where the Doctor's body should be but it has gone. The Dalek's power was low so the shot was not fatal. River rejoins them and tells them that the Doctor lies. He pretended to die so that he could use the time while the others were away to get into the Pandorica. They find him there and River sees that he has wired the Vortex Manipulator to the Pandorica so that he can take it with him when he jumps back to the TARDIS. The light from the Pandorica will explode into every moment in history and restart the Universe. Unfortunately, the Doctor will be on the other side of the cracks. The universe will be restored but the Doctor will never have existed.

He speaks to Amy, telling her to remember her parents who were erased from history by the crack in time in her wall. He pilots the Pandorica into the explosion and resets the Universe.