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 fiancÚ. 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.