The Doctor's worst enemies, The Daleks, The Cybermen, The Angels and The Silence, return, as the doctor's eleventh life comes to a close, and his twelfth life begins.
Orbiting a quiet backwater planet, the massed forces of the universe's deadliest species gather, drawn to a mysterious message that echoes out to the stars - and amongst them, the Doctor. Rescuing Clara from a family Christmas dinner, the Time Lord and his best friend must learn what this enigmatic signal means for his own fate and that of the universe.
- A voice over explains that there is a planet which is broadcasting a mysterious message. This message attracts all the powerful races of the universe, who come to see what the message means.
The Doctor arrives on a spaceship offering peace and comradeship and asking who they are. As an offering, he presents the severed eye stalk of a Dalek. But the ship is filled with Daleks who move to attack him. He calls for "Handles" and is teleported back into the TARDIS.
On the TARDIS, The Doctor has a severed Cyberman head who he refers to as Handles. The Doctor says that even he can't translate the message. Just then, the Doctor gets a phone call from Clara who asks him to pose as her boyfriend while she has Christmas dinner with her family.
The TARDIS materializes outside Clara's flat and she runs inside, finding the Doctor naked. He uses a device to project the illusion of clothes into her mind. When they meet Clara's family, everyone acts oddly and the Doctor explains that he's not broadcasting the illusion of clothes into their minds.
Clara is having trouble cooking the Christmas turkey and they decide to use the TARDIS to help. While inside they return to the planet. Handles identifies the signal as coming from Gallifrey, the Doctor's home world, which is believed to be lost outside the universe. However, the planet is shielded and even the TARDIS cannnot get through.
The TARDIS goes to the Papal Mainframe, which is orbiting the planet, in order to meet with Tasha Lem, the Mother Superior who can authorize them to go down to the planet. While the Doctor and Tasha excuse themselves to talk, Clara has a run in with a Silence.
Tasha Lem explains that they sealed off the planet in order to prevent bloodshed over the signal. She sends The Doctor and Clara down to the planet to investigate the signal. On the planet they have a run in with the Weeping Angles and summon the TARDIS to escape. They then find the quaint town of Christmas. Within this town no one can tell a lie. The Doctor realizes that the truth field is being created by the same signal being broadcast to the universe. He tracks it to the town's bell tower and discovers the same crack which he had originally discovered in Amy Pond's House.
The Doctor realizes that the signal is coming from Gallifrey. They are trying to use the cracks created by the explosion of the TARDIS to gain entry back into the universe. They are waiting for him to speak his true name so they know they have the right place and then reenter. .
The Doctor sends Clara back to the TARDIS which returns her to her home. As it begins to disappear she runs back and grabs onto the outside. Tasha Lem informs the Doctor that the planet he is on is called Trenzalore and that in order to prevent the Time Lords from igniting a new war she and the other races orbiting Trenzalore will destroy the planet if the Time Lords try to come through. She dedicates the church to a new faith: Silence. The Doctor will not be allowed to speak his name. Silence will fall.
What results is a seige, many years long, with the Doctor defending Christmas from incursions by the many enemies orbiting the planet including Weeping Angels, Cybermen, and Sontarans. But a stalemate is maintained by the Doctor's ability to call forth Gallifrey with just a word and by the Papal Mainframe's determination to the destroy the world if he does.
Clara returns many years later to a visibly aged Doctor. He explains that he has used up all his regenerations and that when he dies this time it will be for good. As they talk, Handles, who has served as the Doctor's companion for these years, finally loses power and dies. Tasha Lem invites them for a summit at the Papal Mainframe. On the ship the Doctor explains that the beings known as The Silence are actually confessors for the Church. Their ability to erase memories helps in their function. The group which kidnapped Melody Pond was a rogue faction which sought to avert the standoff by changing the Doctor's history. Tasha Lem explains that the Daleks have become more aggressive and attacked the Papal Mainframe, killing her. She then sprouts a Dalek eye stalk, revealing that her and the others on the ship have been transformed into Daleks. However, when the Daleks spring their trap, Tasha's original personality reasserts itself and helps the Doctor and Clara escape back to Trenzalore. The Doctor sends Clara back home once more.
The Doctor stays in Christmas for hundreds of years, fighting off his enemies and protecting the town. Clara, once again finds the TARDIS outside her flat, this time piloted by Tasha Lem. She is told that the Doctor is near death from old age. Christmas is under a final assault from the Daleks, one which the Doctor doesn't know how to defeat. Once he is dead, they will destroy the planet to prevent Gallifrey from returning.
Clara makes a plea through the crack for the Time Lords to help the Doctor. The crack promptly disappears from the wall and reappears in the sky outside. The Time Lords send a flood of regeneration energy through the crack, allowing the Doctor to regenerate again. The energy of his regeneration is especially violent and allows him to destroy the Daleks and their ship, thus saving Christmas.
Clara boards the TARDIS where she finds the Doctor returned to his younger self. However, he explains that this is only temporary and that he will still regenerate into a new version, the first of a new regeneration cycle. As the regeneration energy begins to consume his body, The Doctor has a vision of Amelia, "the first face this face every saw". He promises to never forget one day of his time as the Eleventh Doctor. He then has a vision of the adult Amy Pond, who gently touches his cheek and says "Raggedy Man, good night."
In snap, the Doctor regenerates into his new form, that of an older, gaunter, man. "I have kidneys!" He exclaims, surprised, "I don't like the color." Just then the TARDIS begins to buck and weave. He tells Clara that they're crashing and asks her "Do you know how to fly this thing?"