5.1 The Eleventh Hour
The failing TARDIS crashlands outside the house of seven-year-old Amelia Pond (Caitlin Blackwood), who welcomes newly regenerated Eleventh Doctor into her house to investigate the crack in her bedroom wall. He must use the TARDIS to regulate its engines, and promises he will return in five minutes which Amelia waits for. However, the TARDIS takes him twelve years into the future, where he joins the adult "Amy" Pond and her boyfriend Rory Williams in capturing the shapeshifting alien known as Prisoner Zerowho has escaped from the crack in Amy's wall and the failure of which will lead to the destruction of Earth by the glactic police force known as the Atraxi. After the Earth is saved, the Doctor tests the newly remodelled TARDIS and accidentally returns for Amy two years later in her timeline, the night before her wedding to Rory, and where she joins him for the promised travels of space and time.

5.2 The Beast Below
The Doctor takes Amy to the distant future, where they explore the Starship UK, a spaceship holding the population of Britain (with the exception of Scotland) after they fled Earth due to dangerous solar flares. They discover that the ship is guided by a Star Whale, who is being tortured out of fear that when let to make its own decisions it will abandon them. Believing that the future cannot go on this way, the Doctor prepares to render Star Whale brain-dead so it will continue to operate the ship but not feel it; however, Amy discovers that it is willing to serve the ship as it could not stand the children crying because of the solar flares.

5.3 Victory of the Daleks
The Doctor and Amy respond to a call from Winston Churchill (Ian McNeice) and visit him during the London Blitz, where he has employed "Ironsides", a scientific creation of Professor Bracewell (Bill Paterson) but which the Doctor recognises as his arch-enemies the Daleks. The Daleks reveal their plan to detonate a device built around Bracewell, who is revealed to be an android, and destroy planet Earth. As the device begins to activate, the Doctor and Amy convince Bracewell that he is human, which deactivates the device.

5.4 The Time of Angels
River Song (Alex Kingston), a woman from the Doctor's future, summons the Doctor and Amy to help her and Father Octavain (Iain Glen) and his group of militarized clerics destroy the last Weeping Angel in the site of the crashed ship Byzantium on the planet Alfava Metraxis. However, it is revealed that all statues in the stone labyrinth where the ship has crashed are Angels and are becoming more powerful from the radiation leaking from the ship. As the Angels surround the group and several clerics are revealed to be dead, the Doctor destroys the gravity globe that had been causing the labyrinth not to be affected by gravity.

5.5 Flesh and Stone
In continuation from "The Timeo of Angels", the group finds themselves thirty feet above at the opening of the Byzantium, which they enter to try escaping from the Weeping Angels. A crack very similar to the one in Amy's bedroom appears in the interior of the ship, which the Doctor discovers erases persons and objects from existance and was caused by an explosion on 26 June 2010. Meanwhile, it is discovered that a projection of an Angel had entered Amy's eye after she had looked into an Angel's eye in the previous episode, and the Doctor intructs her to keep her eyes closed. As the gravity fails, the Weeping Angels fall into the crack, erasing them from history and from Amy's eye, and the Doctor takes Amy to her house on her request. He resists her attempt to seduce him and descovers that the day of Amy and Rory's wedding is 26 June 2010.

5.6 The Vampires of Venice
The Doctor takes Amy and Rory to 16th century Venice as a romantic date, where they meet a man named Guido (Lucian Msamati) whose daughter Isabella (Alisha Bailey) was entered into the House of Calvierri, a school for girls. Guido is distressed because Isabella did not recognise him on the street and bore vampire-like fangs. The Doctor, Amy and Rory investigate the school, where they discover that the city's patron, Rosanna Calvierri (Helen McCrory), is a race of vampiric fish from another planet and has sealed off Venice in attempt to overtake it and make it a place for her race to live after they fled their planet because of the cracks in the universe. She transforms the girls admitted to her school into her race and has ten thousand of her children waiting in the water. Despite the Doctor's reasoning, she activates a storm which will flood Venice, but the Doctor deactivates the device and she sacrifices herself. As they leave, Amy asks Rory to stay and travel with her.

5.7 Amy's Choice
The Doctor, Amy and Rory find themselves travelling between two realities; in one, Amy and Rory are happily married but are being pursued by elderly people possessed by aliens, while in another they are in a powerless TARDIS that will slowly crash into a cold star which will freeze them to death. A man known as the Dream Lord (Toby Jones) says that he has put them in this trap and they must decide which is real and which is fake and die in the false one to wake up in the real reality and escape the trap. When Rory dies in the future reality, Amy decides that it must be fake because she does not want a life without Rory. At the conclusion it is revealed that psychic pollen had entered the TARDIS and caused the dream state, and the Dream Lord is revealed to be a psychic manifestation of the Doctor's dark side and self-loathing.

5.8 The Hungry Earth
The Doctor, Amy and Rory arrive in Wales in 2020, where Dr Nasreen Chaudhry (Meera Syal) and Tony Mack (Robert Pugh) are drilling into the Earth for a mining experiment. Mack's son-in-law, Mo (Alun Raglan), had previously been dragged below the ground, which then happens to Amy. The Doctor discovers that reptilian humanoids the Silurianshave been disturbed by the drilling project and reach the surface, where they kidnap Mo's son Elliot (Samuel Davies). Rory and the Doctor capture one known as Alaya (Neve McIntosh); the Doctor instructs Rory, Tony, and Mo's wife Ambrose (Nia Roberts) to leave Alaya alone as anything done to her may been seen as an act of war. As a Silurian is about to vivisect Amy as he had done to Mo, the Doctor takes Nasreen on the TARDIS below where they discover an immense Silurian civilisation.

5.9 Cold Blood
Amy and Mo escape and discover Elliot is being held in an observation chamber. The Doctor is captured and ordered to execution by Alaya's sister Restac (Neve McIntosh), but Amy and Mo interrupt the trial. They contact Rory, Tony, and Ambrose to inform them they are sending a transport up for they and Alaya, the completion of which will leave them all free to return to the surface. However, Ambrose had killed Alaya out of revenge and they return her body to her people. A deal is made that the Silurians will hibernate for a thousand years as humanity was not ready to share the planet with them. As they leave with Elliot, they find a crack in the cavern which the Doctor reaches into to investigate and pulls out what is later revealed to be a piece of the TARDIS. Before they leave, Restac shoots Rory and he dies and is consumed by the crack, erasing him from existace and Amy's memory altogether.

5.10 Vincent and the Doctor
When visiting a museum, the Doctor finds a creature in the window of a church Vincent van Gogh's The Church at Auvers, and the Doctor takes Amy back to meet Vincent (Tony Curran) and defeat the evil creature. Welcoming them, van Gogh works with the Doctor to find the Krafyis, a lost and blind alien whom only van Gogh can see. Van Gogh kills the creature, though he empathises with its pain. Before leaving, the Doctor and Amy take van Gogh to the present where he discovers that people will admire him, but Amy is devastated to learn that he still committed suicide.

5.11 The Lodger
The TARDIS dematerialises with Amy still inside, leaving the Doctor stranded in present-day Colchester. He tracks the disturbance that caused the TARDIS to behave that way to the second floor of a flat, where people have been persuaded to go up to but have never come down. The Doctor rents part of the downstairs apartment occupied by Craig Owens (James Corden), a man who wishes to confess his love for his close friend Sophie (Daisy Haggard). When Sophie is lured up to the second floor, the Doctor and Craig enter it and discover that it is really a TARDIS-like spaceship disguised by perception filter and has been luring passerby to find a suitable pilot. The fact that Craig does not want to leave counteracts the ship's protocols, and this breaks the ship's hold on the house and allows the TARDIS to land. On the TARDIS, Amy discovers her engagement ring from Rory.

5.12 The Pandorica Opens
River Song summons the Doctor and Amy to 102 A.D. where she shows them a painting by Vincent van Gogh that depics the TARDIS exploding and contains the co-ordinents ofStonehenge. Underneath Stonehenge, they discover a prison box called the Pandorica, which is fabled to contain the most feared criminal in the universe. However, it is revealed that the Pandorica is empty and an Alliance of the Doctor's enemies arrive to put him in the Pandorica as the deadly cracks in the universe were linked to the TARDIS. The trap, which was constructed from Amy's memories, also contains an Auton version of Rory, who shoots Amy. Meanwhile, the TARDIS took River outside Amy's house on 26 June 2010 and explodes, causing the cracks to widen and the universe to begin erasing.

5.13 The Big Bang
The Doctor from the future gives Rory his sonic screwdriver and Rory uses it to get him out of the Pandorica; they place the dead Amy in the Pandorica, which will force her to stay alive once her DNA is given in the form of seven-year-old Amelia in 1996 who places her hand on the Pandorica by way of instructions left by the Doctor. As the universe is collapsing, the Doctor rescues River from the time loop in the exploding TARDIS and realises that if he flew the Pandorica, which contains a restoration field, collided with the exploding TARDIS it would restore the universe as it should have been, though this process erases him from history and closes the cracks. However, Amy is able to bring him back at she and Rory's wedding due to something the Doctor told her as he was being erased, and the newly wedded couple continue to travel with him.