The Doctor and Amy Pond  travel to the oldest planet in the universe where a legendary message turns out to be another "calling card" of River Song. Following the coordinates from the message, they arrive at Roman Britain in 102 AD and find River posing as Cleopatra. River explains that she has received warning of the destruction of the TARDIS from a painting by Vincent van Gogh ("Vincent and the Doctor") that in 1941 reached Winston Churchill and Professor Bracewell ("Victory of the Daleks"). Churchill had attempted to warn the Doctor himself, but the TARDIS instead connected his call to River; she subsequently escaped from prison and encountered Liz 10 ("The Beast Below"), who had Van Gogh's painting in her collection, and then used a vortex manipulator to transport herself to the oldest planet then to the coordinates in the painting. The Doctor realises the painting and destruction of the TARDIS may be connected to the "Pandorica", a fabled prison for the universe's deadliest being, and rationalises that it must be stored in a memorable location, the site of Stonehenge.

At Stonehenge, the Doctor, Amy, and River find a passage to an underground area, which the Doctor terms "the Underhenge". Inside, they find the Pandorica, a room-sized metal box outfitted with every type of lock imaginable. The Doctor and River become concerned when they discover that the Pandorica is opening from inside and transmitting a message across time and space, drawing many of the Doctor's foes to Earth. River warns that "everything that ever hated [the Doctor] is coming tonight". The Doctor refuses to flee and instead asks River to seek help from the nearby Roman legion while he remains with the Pandorica. She finds the legion's commander reluctant, though one mysterious centurion and fifty others do volunteer.

Back underground, while Amy questions the Doctor about the engagement ring she has found, the pair are attacked by the debris of a Cyberman's suit trying to find a new host. The Doctor is stunned and Amy sedated with a flechette. She runs away and is rescued by the mysterious centurion, who turns out to be Rory Williams. The revived Doctor is baffled to find Rory alive, since he is supposed to have been erased from history by a crack in the universe ("Cold Blood"). Rory is even more confused and says he simply remembers dying one second and being a Roman soldier the next.

As more enemies gather in orbit, the Doctor temporarily delays the aliens and instructs River to bring the TARDIS to Stonehenge. Although shown to be an expert TARDIS pilot ("The Time of Angels"), River now finds the machine impossible to control and gets locked on course for Amy's house on 26 June 2010 - the very date of the time energy explosion that caused the cracks in the universe ("Flesh and Stone"). Whilst she ventures outside, the scanner screen suddenly cracks into the same shape as the other cracks in the universe, while an ominous voice declares "silence will fall". River finds large burn-marks on the lawn, and then begins to explore Amy's bedroom, still full of representations of the Doctor and the TARDIS. She also finds elements such as Pandora's box and the Roman soldiers within Amy's drawings and books. She relays this to the Doctor, who starts to worry they might all be imaginary constructs taken from Amy's mind to entrap him, and believing their own cover story until they are activated.

Rory meanwhile has an emotional conversation with Amy as he tries to connect with her using the engagement ring that he had left aboard the TARDIS, but she is still unable to remember him. The TARDIS begins to malfunction dangerously. Upon discovery of the date to which River has been taken, the Doctor orders her to get out of that timezone, but the TARDIS is now controlled remotely. He urges her to get out, as the TARDIS engines are supposed to shut down automatically when no one is on board, but she finds herself locked in.

Suddenly, Rory and the 'legionaries' with the Doctor are activated: they are Autons. The Rory Auton remains with Amy, struggling to retain his human consciousness and stop himself from killing her. Shortly after she remembers who he is, he loses control and shoots her. Meanwhile, the other Autons capture the Doctor and take him to the now-open Pandorica, which proves to be empty. Daleks, Cybermen, Sontarans, and other enemies arrive and reveal that they have formed an alliance and built the Pandorica as a prison for the Doctor, as they believe he is about to destroy the universe. The Doctor pleads that they have made a mistake and the TARDIS, not him, is about to destroy the universe but the aliens refuse to believe that anyone else can pilot the TARDIS.

River frantically manages to hot-wire the TARDIS door, but finds her way blocked by a stone surface. She declares, "I'm sorry, my love," as the TARDIS goes critical and explodes. Rory is still cradling the lifeless Amy. The Pandorica closes on the Doctor, and a dramatic reveal shows explosions surrounding the Earth, which slowly fades to black as silence falls.

Following from the cliffhanger of the previous episode, the Doctor is sealed in the Pandorica, a prison designed for him by his greatest foes and baited by elements of Amy's childhood imagination, while River Song is trapped in the TARDIS as it explodes, triggering the end of the universe. As the episode begins, the Earth, Moon, and what appears to be the Sun are all that remain in a starless black void. In 102 AD, the Auton replica of Rory, having shot Amy, is still holding her lifeless body when a future version of the Doctor, using a Vortex Manipulator, briefly appears and gives Rory his sonic screwdriver, with instructions to open the Pandorica. Rory releases the imprisoned Doctor, who places Amy inside the Pandorica where she will be revived and held in stasis. Rory, ageless due to his Auton nature, stays with the Pandorica, guarding it through nearly two millennia and creating a mythology around the box that survives to the present day.

The Doctor jumps forward in time to 1996, and provides hints to the young Amelia Pond—who has dreams of a star-filled sky—that lead her to the British Museum, where the Pandorica is on display. Amelia's touch opens the Pandorica, releasing her older self. Rory, now a security guard at the museum, arrives just in time to save the Doctor, Amy and Amelia from a fossilized Dalek. After an emotional reunion, the Doctor uses the Vortex Manipulator to pass his screwdriver to Rory in the past and rescue River from the TARDIS. The group flees through the museum, purused by the Dalek, which the Doctor surmises has been re-activated by the light of the Pandorica. They meet a mortally wounded version of the Doctor from twelve minutes in the future, who whispers something to his past self and dies. The Doctor explains that a fragment of the original, star-filled universe is inside the Pandorica, and if they can transfer it to every point of the collapsing universe simultaneously, they may be able to "reboot" reality. He is then shot by the Dalek, and jumps twelve minutes into the past. Rory and Amy escape, while River confronts the Dalek- which uncharacteristically begs for mercy when told her name.

After jumping back twelve minutes, the Doctor did not die, but instead directed his earlier self to create a diversion, giving the wounded Doctor the opportunity to program the Pandorica to fly into the Sun-like source of light: the TARDIS, exploding simultaneously at every point in space and time. When his companions return, the Doctor explains that once the universe is rebooted, Amy—having lived near the cracks in the universe all her life—will be able to use her memories to restore people who have been erased, and that he himself will be trapped in the void between universes once the cracks close. The Doctor then pilots the Pandorica into the TARDIS explosion, creating a second Big Bang and returning the universe to normal.

The Doctor then finds himself rewinding through his life as an observer. Amy can hear but not see him, and as he passes through the events of "Flesh and Stone", he takes advantage of her closed eyes to tell her to remember what he told her when she was seven years old. Arriving on the day he met Amelia Pond ("The Eleventh Hour"), he finds the young girl asleep outside, waiting for her "raggedy Doctor" to return. The Doctor carries her to bed, and tells her a story about a daft old man who stole—"well, borrowed"—a magic box that was "big and little at the same time. Brand new and ancient. And the bluest blue ever." He then steps into the crack in Amelia's bedroom wall, sealing it completely.

Amy wakes up on 26 June 2010, the day of her wedding, to find she has remembered her mother, father and the human Rory back into existence. During the wedding reception, however, she feels as if she is forgetting something. When she sees River Song's diary, its cover fashioned after the TARDIS, she tearfully recalls the Doctor's story of "something old, something new, something borrowed and something blue", causing the Doctor and the TARDIS to be restored. The Doctor joins in the wedding celebration.

After the wedding, the Doctor gives River the Vortex Manipulator to return to her time. River sadly warns him he will soon learn who she truly is, and that it will change everything. Aboard the TARDIS, the Doctor explains to Amy and Rory that unanswered questions remain about the destruction of the TARDIS and the nature of "the Silence" that will fall, but before they can contemplate that, the Doctor receives a telephone call alerting him to the presence of an escaped Egyptian goddess on the Orient Express in space. Rory and Amy decide to join him, and the three leave on their next adventure.
[edit] Continuity

The episode revisits several scenes from earlier in the series. The first scene in the episode mirrors the start of "The Eleventh Hour", except this time the Doctor does not crash into Amelia's garden, instead appearing later to direct her to the museum. Upon the TARDIS's restoration Rory tells Amy's parents that "I was plastic" and that the Doctor was "the stripper at my stag do", the latter event having been seen in "The Vampires of Venice".

As the Doctor rewinds through his life, he sees events which relate to "The Lodger", but which were not shown in that episode. His conversation with Amy during the events of "Flesh and Stone" appeared in that episode, though it was not clear that this was a Doctor from a different timeline. Finally, he arrives in seven-year-old Amelia's house the night she waited for him in "The Eleventh Hour".

Early in the episode, Amy's aunt states that she does not trust Richard Dawkins (who appeared as himself in "The Stolen Earth") due to his support for the existence of stars. When the sonic screwdriver given to Rory and that in the pocket of the Doctor in the Pandorica touch they cause sparks, in a revived-series reference to the Blinovitch Limitation Effect.