The main story arc of the series focused on the significance of the character of Clara, whom the Doctor had encountered twice before as Oswin in "Asylum of the Daleks" and as a governess in "The Snowmen". It also features the recurring appearance of the Doctor's enemy, The Great Intelligence.
Kidnapped by his oldest foe, the Doctor is forced on an impossible mission - to a place even the Daleks are too terrified to enter... the Asylum. A planetary prison confining the most terrifying and insane of their kind, the Doctor and the Ponds must find an escape route. But with Amy and Rory’s relationship in meltdown, and an army of mad Daleks closing in, it is up to the Doctor to save their lives, as well as the Pond’s marriage.
An unmanned spaceship hurtles towards certain destruction - unless the Doctor can save it, and its impossible cargo... of dinosaurs! By his side a ragtag gang of adventurers; a big game hunter, an Egyptian Queen and a surprised member of the Pond family. But little does the Doctor know there is someone else onboard who will stop at nothing to keep hold of his precious, prehistoric cargo.
The Doctor gets a Stetson (and a gun!), and finds himself the reluctant Sheriff of a Western town under siege by a relentless cyborg, who goes by the name of the Gunslinger. But who is he and what does he want? The answer seems to lie with the mysterious, Kahler-Jex, an alien doctor (yes another one!) whose initial appearance is hiding a dark secret.
The Doctor and the Ponds puzzle an unlikely invasion of Earth, as millions of sinister black cubes arrive overnight, almost like presents falling from the sky. But what are they, what’s inside them and most importantly, who sent them? With the international community at a loss, it’s left to the Doctor to unearth who is behind the mystery.
The Doctor’s heart-breaking farewell to Amy and Rory – a race against time through the streets of Manhattan, as New York’s statues come to life around them… With Rory’s life in danger, the Doctor and Amy must locate him before it’s too late! Luckily, an old friend helps them and guides the way.
When the Doctor receives a mysterious call from Clara, the woman that he's been seeking since he has seen her die twice, he arrives in 21st century Earth and discovers that something is using wi-fi to download human minds into the Internet... and feed on them.
Clara wants to see something awesome, so the Doctor whisks her off to the inhabited rings of the planet Akhaten, where the Festival of Offerings is in full swing. Clara meets the young Queen of Years as the pilgrims and natives ready for the ceremony. But something is stirring in the pyramid, and a sacrifice will be demanded.
The Doctor and Clara land on a damaged Russian submarine in 1983 as it spirals out of control into the ocean depths. An alien creature is loose on board, having escaped from a block of Arctic ice. With tempers flaring and a cargo of nuclear weapons on board, it’s not just the crew but the whole of humanity at stake!
Clara and the Doctor arrive at Caliburn House, a haunted mansion sat alone on a desolate moor. Within its walls, a ghost hunting Professor and a gifted psychic are searching for the Witch of the Well. Her apparition appears throughout the history of the building, but is she really a ghost? And what is chasing her?
When a salvage ship attempts to pull the TARDIS aboard when the time vessel's shields are down, an explosion occurs. The Doctor forces the salvage crew to help him find Clara, who is lost somewhere inside his vessel.