In space, a message is being broadcast that is drawing alien fleets-Daleks, Cybermen, Sontarans and others-to it. The Doctor-with the help of a body-less Cyberman named “Handles”-tries to figure out what it is.
Picking up Clara, he arrives at one of the other ships-the Papal mainframe, a kind of futuristic church, to help them investigate the strange message, while the planet is protected by a force field. However, there are Silents onboard the ship, although neither the Doctor nor Clara remembers seeing them because of their powers. Paradoxically, Handles also identifies the planet as Gallifrey, although Gallifrey is in another universe…
The Doctor and Clara go down to the planet-after avoiding a group of Weeping Angels-and discover the town called Christmas, which has a ‘truth field’ where no one can tell a lie. He also discovers the name of the planet-Trenzalore, although a millennia before his last fateful visit-and the origin of the signal. It’s from Gallifrey, saying “Doctor Who?” asking for his real name-communicating to our universe through one a reopened crack in time from his first season.
The Time Lords want to return to ‘our’ universe. Only problem is, if they do, the Time War will begin anew, and the innocents of Trenzalore will likewise be caught in the crossfire as well. The Papal mainframe becomes the Church of the Silence to prevent the Doctor from speaking his name and letting the Time Lords through, setting off a chain of events that of course will lead up to the events of the earlier Matt Smith season (although this is mainly the work of a breakaway faction that destroys the TARDIS creates River Song and “kills” him).
The Doctor sends Clara back and becomes the protector of Christmas, fighting off the various races. Clara eventually is able to return, but by the Doctor’s POV, it’s been 300 years. His once-young body-which at this point is 500 years old-is starting to visibly age. Handles has also ceased to function, and the Doctor reveals to Clara that he’s actually on his last life-he’s used up all twelve regenerations a time lord is allowed to have, and once his current body dies, that’s it. He also believes it will be his end due to seeing the future damaged TARDIS and timestream in the future Trenzalore.
What’s worse, the Daleks want to battle their old enemies and destroy them once and for all, and have taken over the Papal mainframe too, although at least their leader, Tasha Lem, is able to mostly resist.
The war continues, and Clara is set back once again. Finally, it’s the Doctor and what’s left of the silence against the Dalek fleet. Tasha brings Clara back to Trenzalore, where the Doctor has aged another few centuries, and now has the appearance of an elderly man, not too much unlike his very first incarnation.
The Doctor heads to finally face the Daleks, as a last of sorts. Clara however, tells the Time Lords that they don’t need to really know his name-only that he’s the Doctor-the only name he needs-and that he needs their help.
The Time Lords close the crack-and then open another between the Dalek fleet and the Doctor. Only this time, it’s no signal they’re sending.
…..but the energy that time lords needs to regenerate. They’ve given the Doctor a new lease on life-another set of regenerations.
The regeneration energy is also enough for the Doctor to destroy the Dalek fleet as well.
The Doctor returns to the TARDIS, with the process of regeneration begins in front of Clara, and he briefly re-assumes a younger appearance as a reset before the big change. He hallucinates Amy and says he was quite fond of this current life, but change is good too.
Bidding farewell to the hallucination of Amy, and his “cool” bow tie….
He regenerates once again.
…into a stunned looking, middle-aged man, who’s got new kidneys, but doesn’t like their color.
Clara’s a bit stunned too. Despite knowing about regeneration and stuff, she didn’t quite expect him to turn out like this.
Also the TARDIS is crashing, and he has no idea how to fly it!
“Just one question…do you have any idea how to fly this thing?”