The Time of the Doctor (TV story)

The Time of the Doctor was the 2013 Doctor Who Christmas special. It was the 800th episode of the series and the final appearance of Matt Smith as the Eleventh Doctor. It served as a conclusion to the entirety of the Smith era, bringing back both the Silence and Trenzalore and bringing their stories to a close. Karen Gillan also made a surprise cameo as a hallucination of Amy Pond, rounding out Smith's era.

The special tackled an issue that hadn't been talked about since the series came back in 2005: that of the limited amount of regenerations, introduced in The Deadly Assassin. It confirmed that the Doctor had actually used up all twelve of his possible regenerations, before being granted a brand new regeneration cycle at the end of this story. It also served as Peter Capaldi's formal introduction as the new Doctor, after making a surprise cameo appearance in The Day of the Doctor.

The special marked the departure of producer Marcus Wilson, finishing his work with the series after Matt Smith's final scene was filmed.

Synopsis
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. Among them, the Doctor. Rescuing Clara from a family Christmas dinner, the Time Lord and his companion must learn what this enigmatic signal means for his own fate and that of the universe.

Plot
The Doctor is among thousands of ships orbiting a planet after hearing a message being broadcast from it, a message that no-one can understand. He visits a ship, holding a Dalek Eye Stalk to show his bravery. Unfortunately, the ship belongs to Daleks, who fire at him until he teleports back to the TARDIS, where a disembodied Cyberman head that he calls "Handles" is plugged into the console. Clara calls the Doctor via the TARDIS phone, and pleads that he pretend to be her boyfriend for her family's Christmas dinner. The Doctor then accidentally visits a Cybership while holding Handles, where he is also shot at until he returns to the TARDIS again.

The Doctor picks up Clara from her home (after causing major embarrassment when he forgets to update his holographic suit to be visible to her family) and after placing her Christmas turkey into a device that will either cook it or bring it back to life, takes her to the planet's orbit. When asked to identify the planet, Handles claims it is Gallifrey, which the Doctor refutes. The two are invited aboard the Papal Mainframe, a space church headed by Mother Superious Tasha Lem, with Clara getting a pill from the Doctor to make her appear naked in the church (nudity in the Papal Mainframe is considered a mark of respect). Tasha and the Doctor discuss the signal coming from the mysterious planet, while Clara repeatedly sees and forgets several Silents that surround her. She bursts into the room where the Doctor and Tasha are conversing, but forgets why after she does so.

Tasha sends the Doctor and Clara to the planet, but accidentally places them in the middle of an ambush by Weeping Angels. They escape to a town called Christmas, surrounded by a truth field, so no one can lie. Here the Doctor finds a crack in time through which the message is being broadcast. Using a copy of the Seal of the High Council he once took from The Master in the Death Zone, he has Handles translate it. The message is a repeat of the same question: "Doctor who?" The Doctor realises that this is the Time Lords, trapped in the pocket universe he and his previous selves sent them to, trying to get out. If the Doctor speaks his real name, the Time Lords will know they are in the right place and come through, and all the alien species above will descend on the planet and begin the Time War anew. Tasha contacts the Doctor, telling him this cannot happen and the Doctor refuses to withdraw and let his enemies destroy the planet, which she reveals to be Trenzalore – the place where he is supposed to die.

The Doctor tricks Clara into plugging a device into the TARDIS that transports her home. For the next three hundred years, he defends Trenzalore from his enemies. He defends Christmas in a number of ways. One time he disabled the cloaking device on a Sontaran vehicle, allowing the Church to destroy it. On another occasion, he tricked a wooden Cyberman, created to be too primitive to set off the alarm, into destroying itself after using both the sonic screwdriver and the truth field to make it think its gun had been turned around. According to Tasha, the Doctor seemed to forget of life before the siege. He spent his spare time fixing the toys the children played with - sometimes a little too much - and grew close to a child called Barnable.

Clara returns after gripping to the sides of the TARDIS, which forces the TARDIS to increase the shields and bring her back through the Time Vortex, slowing it down considerably. She meets a Doctor who has spent three centuries defending the town of Christmas. He now has grey hair and wrinkles, and needs a walking stick. The Doctor and Clara at first exchange angry remarks - Clara is strongly upset about being left behind without even a good-bye, and the Doctor becomes irritated that she returned to Trenzalore. However, the two of them can't help but embrace in a warm hug.

The Doctor decides to take Clara to his new home on Trenzalore, the bell tower in Christmas. He has taken residence in the same room with the time crack, now adorned with hundreds of drawings given to him by the children of Christmas. Each drawing shows a child's love for the Doctor and provides a peek back at his bygone adventures, after recounting many stories over the passing centuries to entertain the kids. However, Handles has heavily aged alongside the wearisome Doctor and barely functions. The rusted Cyberman head announces he has developed a fault through his stuttering electronic voice, warning that he doesn't have much time left.

Shortly after, Handles dies – but not before finally reminding him that he needs to patch the TARDIS phone back into the console. The Cyberman ceases to function, and the Doctor despairingly shakes his head. He quietly says, "Thank you, Handles, and well done. Well done, mate."

The sun rises over Trenzalore, and the Doctor informs Clara that he watches the sunrise every day to remind himself of what he is protecting. Though she thinks it is a beautiful sight, Clara is pressed to ask the Doctor why he decided to drop her back on Earth. The Doctor feared that if he had allowed her to stay, he'd outlive her or lose her in battle, and he would have buried her long ago. Clara defiantly tells the Doctor she would have found a way to prevent him from being stuck on Trenzalore, but the Doctor is quick to disagree; "Everyone gets stuck somewhere eventually, Clara. Everything ends." Clara still isn't convinced it applies to the Doctor, even though he has grown quite old. She says he cannot die, and instead regenerates with a new face each time he is about to perish. The Doctor grimly reveals to her that Time Lords can only regenerate twelve times. She surmises that this shouldn't be a problem, as he is the "eleventh Doctor". He reminds her of "Captain Grumpy", his Time War incarnation; although he didn't call himself "the Doctor", it still counted as one of his lives. So, too, did the regeneration used by the Tenth Doctor during his Meta-Crisis. He is therefore on his thirteenth, and final life. He and Clara then watch the sun rise for a few minutes, until a thunderous boom from overhead reveals Tasha Lem's holographic face in the sky. She announces to the Doctor that the newly-renamed Church of the Silence is requesting parley. The Doctor is being allowed to meet with her to discuss a truce, with his rights and safety sanctified. Tasha offers to have him transported to the Papal Mainframe, but the Doctor declines, knowing he's got his TARDIS back. After Tasha deactivates her hologram, the sun has already vanished over the horizons of Trenzalore. The Doctor reminds his companion, "Everything ends, Clara. And sooner than you think."

The Doctor and Clara prepare to board the TARDIS, where they find Barnable guarding it, wondering if the Doctor will leave Christmas. He gives the boy assurance that he's known the Doctor long enough to trust he will return. Barnable promises to wait for him. Clara and the Doctor then arrive back on the Papal Mainframe, now converted into the Church of the Silence, where Tasha still remains in power as a youthful Mother Superious. When Clara mentions her youthfulness, the Doctor simply replies that she is "against" aging. After centuries of battle with the Church, the Doctor now understands the origin of the Silents. The memory-proof race of aliens are genetically-engineered confessional priests, whom Church members can confess their sins to, then later forget. When the Doctor returns to Tasha's chapel, he discusses the parlay at a table instead of a bed (as seen when he first arrived at the Papal Mainframe). Tasha explains a renegade faction of the priests belonging to a sect of the Church called the Kovarian Chapter broke away and travelled back in time to stop the Doctor from reaching Trenzalore. However, Tasha has been helpless against the onslaught of the Doctor's enemies since his long battle began. The Mainframe itself was attacked by the Daleks three days prior to their meeting. The Doctor asks why she didn't call for help. Tasha replies, "I tried. I died in this room, screaming your name. Oh... I died. It's funny the things that slip your mind..."

With those words, the horrified Doctor realises that Tasha and her crew have been killed by the Daleks and turned into Dalek puppets. Eyestalks burst out from their skulls - even the Silents. This is a trap set by the Daleks to snare their greatest enemy. As Tasha succumbs to the puppet conversion, three Daleks enter the chapel and accost the Doctor. He is surprised that they now remember who he is, after Oswin Oswald purged the Dalek Pathweb of their information about him. The Daleks have reasserted their memories after harvesting replacement information from Tasha Lem's cadaver. Because of this, the Daleks have redoubled their efforts to stop him from saving Gallifrey, well aware their nemesis race, the Time Lords, could return to wipe them out. The Doctor prepares to surrender, allowing the Daleks to think he would let Clara be exterminated. Clara plays along with the bluff, realising the Daleks would kill her even if he tried to save her rather than betray. The Doctor then praises Clara for being a strong-willed woman, but also berates Tasha, claiming her church was useless and she was too spineless to be of any help to him in the war. The insults urge Tasha to regain her mind, subconsciously furious at the Doctor, giving him a fierce slap. She then uses her puppet form's gunstick to wipe out the Daleks. The Doctor kisses her and apologises for having to make her angry, encouraging Tasha to keep fighting back the Dalek reprogramming still inside her. As he and Clara escape to the TARDIS with Tasha's help, Tasha protests that she has kept fighting for the sake of the peace, not the Doctor and his ego.

Inside the TARDIS, a timer bell dings, alerting the Doctor that Clara's turkey has finished cooking - or woken up. Before Clara goes to check on it, she asks the Doctor to promise her he will never leave her behind again. He complies. As she goes down to the lower level, the Doctor sees Barnable still beside his TARDIS. The Doctor quietly replaces the charger inside the TARDIS and returns to Christmas town. While Clara thinks he has stepped out, she exits the TARDIS with turkey in hand only to find that she is back on Earth. He has tricked her into leaving his company for the second time, and the TARDIS soon makes a return flight to Trenzalore right after she exits it with her cooked turkey. This time, she really is stranded without any means of return.

On Trenzalore, Barnable questions why the Doctor has brought back his TARDIS if he doesn't intend to leave the planet. He explains it is a reminder that he might leave someday.

The Doctor continues his long war against his enemies, as a great many years pass. Now on good terms with the Church again, he is able to ally with their soldiers and Silents instead of facing them as villains. Together they defend the planet from attackers above, until only the Daleks are left. The troops of the Church help the Doctor defend Christmas against aerial attacks by fighter pods and land assaults from Dalek tanks. Countless casualties mount up, but the Doctor maintains his stand on Trenzalore.

Meanwhile, having returned to her family (who assume she's broken up with her "boyfriend"), Clara asks her grandmother about her late husband, who consoles her with memories of him. Clara cries when she notices how similar they sound to her own memories of being with the Doctor. She then hears the TARDIS engines and joyfully runs outside, thinking the Doctor has changed his mind. Instead, she finds the TARDIS piloted by Tasha, claiming, "Flying the TARDIS is easy... it's flying the Doctor that's hard." She returns Clara to Trenzalore to see the Doctor one last time, saying she could not let him die alone.

Clara reenters the Doctor's old sanctuary in the bell tower to find an elderly man toiling away at fixing a child's wooden horse. After announcing her presence to him, he turns around to reveal a heavily wrinkled face with long, balding white hair, glasses perched on his weakening eyes. The Doctor is now very old and often acts slow and slightly confused. He still won't release the Time Lords, knowing that it would mean Hell for all the universe. All his enemies have withdrawn save for the Daleks, whom he has been fighting with the aid of the Silence. The Daleks launch their final attack and the Doctor, finally out of ideas, weapons and regenerations, goes to meet them. He asks Clara to stay hidden and safe, calling it "one last victory". After he leaves, Clara returns to the crack in time, pleading with the Time Lords to save the Doctor, saying: "His name is the Doctor! All the name he needs, everything you need to know about him, and if you love him - and you should - help him!". The crack suddenly vanishes.

At the top of Christmas's clock tower, the Doctor is preparing to die. He admits defeat to the Daleks, and jests that it took them so long to plot a proper way to kill him that he's doing it himself by dying of old age. Then the crack appears in the night sky and through it, energy emanates out to the Doctor. The Daleks begin to taunt him: "The rules of regeneration are known! You have expended all your lives!" The Doctor notices regeneration energy building inside him: the Time Lords have granted the Doctor a new cycle of regenerations. He defies his enemies, boasting that his unprecedented thirteenth regeneration is "breaking some serious science" and is "gonna be a whopper"! As his regeneration process begins, Christmas town's clock strikes twelve. The Daleks begin to panic as they realize he is regenerating, and the Doctor triumphantly roars: "If you want my life - Come. And. GET IT!" He whips his arms around and channels his regeneration energy to destroy the Daleks and their ship. With a final, devastating blast to the Dalek gunship, he shouts into the sky: "Love from Gallifrey, boys!" An enormous explosion results from this regeneration energy, wiping out every single Dalek attacking the planet.

In the aftermath of the Doctor's regenerative backdraft, the villagers of Christmas emerge from hiding. Clara quickly returns to the TARDIS in search of the Doctor. She sees his worn out winter clothes splayed on the TARDIS console floor, while fish fingers and custard sit on the control panel. She hears footsteps coming up the stairs. She turns to see the Doctor, with his current incarnation's youth restored and dressed in his normal clothes. The Doctor informs Clara that this is "a reset". The process of change has started and cannot be stopped. He enjoys a taste of the fish custard, a meal he enjoyed at the very start of his now fading incarnation. Clara is saddened greatly when she realises that the Doctor she knew is about to disappear. However, the Doctor is not upset about the regeneration yet to come. He understands how fast everything about him and life itself can be gone in a moment, because it is always changing. He comforts Clara by telling her that times change, and so must he. The Doctor's hand begins to glow with regenerative energy and he smiles.

Suddenly, he sees a little girl running through the balcony of the TARDIS with cheerful giggling, with every inch of its walls covered in her drawings of their adventures together, alongside those given to him by the children on Trenzalore. Aloud, he calls out to Amelia. Clara asks who Amelia is, and he describes her as "the first face this face saw." Happily awaiting the regeneration, the Doctor gives this incarnation a fond eulogy. He assures Clara, "We all change, when you think about, we are all different people, all through our lives, and that's okay, that's good, you've gotta keep moving, as long as you remember all the people that you used to be. I will not forget one line of this, not one day, I swear. I will always remember when the Doctor was me." He then sees an adult Amy Pond in the TARDIS. Amy descends from the balcony, places her hand against his cheek, and tells him, "Raggedy Man... good night."

The Doctor places his hand against her face as well, only to see he's reaching out for air. Ready to move on and become a new man, the Eleventh Doctor removes his cherished bowtie, dropping it to the floor. In tears, Clara begs him not to change and reaches out to him. Extending his had towards her, he smiles wearily and whispers "Hey...", and then suddenly jerks his head back.

In barely a second's time with a flash of golden light, the Doctor has completely changed from the youthful alien Clara knew, to an older-looking man with curled silver hair and the impeccable razor-sharp gaze of the Doctor that joined the previous twelve to rescue Gallifrey from the Time War. Utterly dumbfounded by this new face, Clara can only watch open-mouthed as the Doctor stares her right in the eyes, before keeling backward, clutching his waist. He proclaims, "Kidneys! I've got new kidneys! I don't like the colour..." Bewildered, Clara asks if it's the colour of his kidneys he doesn't like. Suddenly, the TARDIS begins shaking. The new Doctor not only tells her that they're crashing into something, but to her horror, he says he has just one more question - "Do you happen to know how to fly this thing?"...

Cast

 * The Doctor - Matt Smith
 * Clara - Jenna Coleman
 * Tasha Lem - Orla Brady
 * Dad - James Buller
 * Linda - Elizabeth Rider
 * Gran - Sheila Reid
 * Colonel Albero - Mark Anthony Brighton
 * Abramal - Rob Jarvis
 * Marta - Tessa Peake-Jones
 * Barnable - Jack Hollington
 * Colonel Meme - Sonita Henry
 * Handles' Voice - Kayvan Novak
 * Young Man - Tom Gibbins
 * Voice. - Ken Bones
 * Cyberman - Aidan Cook
 * Voice of the Daleks & the Cybermen - Nicholas Briggs
 * Dalek 1 - Barnaby Edwards
 * Dalek 2 - Nicholas Pegg
 * Silent - Ross Mullan
 * Sontaran - Dan Starkey
 * Weeping Angel - Sarah Madison
 * Wooden Cyberman - Daz Parker (uncredited)
 * with Karen Gillan as Amy Pond, and introducing Peter Capaldi as The Doctor

Species

 * Amongst the species massing at Trenzalore in response to the mysterious signal are the Daleks, the Cybermen, the Judoon, the Sontarans, the Silurians, the Terileptils and the Raxacoricofallapatorians.
 * The Cybermen are shown to use the Cybus phrase "Delete" in one of the drawings.
 * The Doctor traps a Weeping Angel with a mirror so that it is forced to look at itself.
 * A puppet of a Monoid is seen.
 * A drawing of what may be one of the Racnoss and a Pyrovile hangs on the wall of the clock tower.
 * A drawing of an Ood and some Adipose hangs on the wall of the clock tower.
 * The Doctor mentions an instance when he arm-wrestled a Draconian.
 * The Doctor says it is July in the town of Christmas, which nods to phrase "Christmas in July", a whimsical tradition on Earth to celebrate winter-themed festivities to offset the hot climate of summer.
 * When the Doctor protests about not being given pink marshmallows, Tasha reasons they have too many E numbers (artificial additives), and the Doctor is "hyper(active) enough as is".

Story notes

 * This is the first televised regeneration story in which the Doctor regenerates at the end of the story to end on a shot of a character other than the Doctor and the second since The War Games not to end on the Doctor's new incarnation. In this case, this story's final frame shows Clara's reaction to the newly regenerated Twelfth Doctor, not the Twelfth Doctor himself.
 * This story takes place over a longer amount of time than any other, with the Doctor having lived more than three hundred years (and probably far more) since the beginning of the episode.
 * This is the shortest regeneration story (in overall run time) to be broadcast on BBC1, as The Night of the Doctor was only shown on Red Button.
 * The regeneration is presented differently from other regenerations shown in the revived series, with the use of a prolonged explosion of energy occurring before the actor transitions. The final transition consists of a brief flash of golden light around the actor's head.
 * Regenerations in the revived series are presented as getting bigger and stronger each time. The Ninth Doctor's regeneration into the Tenth Doctor's introduced the regeneration flames. The Tenth Doctor's regeneration into the Eleventh Doctor's used the same effect but as a result of holding it in for too long, causes damage to the TARDIS. When the Eleventh Doctor's regenerative abilities are reset into a new cycle, the effect is big enough to destroy a Dalek ship. However, when the first regeneration after the reset completes itself (the physical change from Eleventh to Twelfth), it is shown as a simple transition.
 * This episode reuses music from TV: The End of Time, another regeneration story. As Clara approaches the building where the elderly Doctor waits, the piece "Four Knocks" can be heard. The piece had been used in the previous regeneration story as the Tenth Doctor rages about his impending death to a trapped Wilfred Mott, which preempts his eventual regeneration.
 * Before filming for this special began in September 2013, Matt Smith agreed to play a role in the American film, How to Catch a Monster. His character was depicted as having a thug-like buzz cut, which meant Smith had to have his signature quiff completely shorn off. By the time the filming was underway for the special, Matt's hair had not grown back enough to fill out the Eleventh Doctor's hairstyle. It was decided that he would use a hairpiece identical to his quiff, which also made it easier for makeup artists to apply ageing effects through older-looking hairpieces. In a humorous moment in the episode that references the wig, the Doctor, surprising Clara, removes a wig to reveal he is bald. (A cap was used to achieve the effect)
 * During the filming of the special, Matt Smith suffered an injury to his leg and later had to visit a physical therapist to recuperate from the accident. This injury inspired a rumour that the script for the special would be altered to have the Eleventh Doctor lose a leg when the Weeping Angels attacked. The rumour was proven false when no such event took place in the episode. However, Smith is seen using a cane in a number of scenes and his mobility prior to regeneration is noticeably limited; in both cases these factors were worked into the storyline.
 * This is both the second Christmas special and the second regeneration story to feature the Cybermen, being preceded by The Next Doctor in 2008 and The Tenth Planet in 1966 respectively. It is also the third regeneration story to feature the Daleks, the first being The Parting of the Ways in 2005 and the second being The Day of the Doctor in 2013. The show's very first Christmas episode, "The Feast of Steven" in 1965, was also part of The Daleks' Master Plan but the Daleks were notably absent from that particular episode. This is the eighth story overall to feature both Daleks and Cybermen in the same episode with major roles, preceded by The Five Doctors, The Ultimate Adventure, Army of Ghosts/Doomsday, The Pandorica Opens/The Big Bang, Return to Earth, The Mazes of Time and The Eternity Clock.
 * Additionally, Daleks, Cybermen, Sontarans, Silurians, Judoon and Slitheen were all part of TV: The Pandorica Opens; Cybermen, Sontarans, Silurians and Judoon were all part of TV: A Good Man Goes to War; and Daleks, Cybermen, Silurians and Silents were all part of GAME: The Eternity Clock.
 * Moreover, Daleks and Sontarans were both part of AUDIO: The Five Companions; Daleks and Silurians were both part of GAME: Evacuation Earth; and Daleks, Cybermen and Silurians were all part of GAME: The Mazes of Time.
 * This is despite the fact that Steven Moffat said he had no desire to write a story in which the Doctor faces all of his enemies (REF: The Brilliant Book 2011) yet he is the writer that has come closest to doing this after writing three episodes now which have featured multiple recurring enemies.
 * With their role in The Day of the Doctor, this marks the second time the Daleks have featured in two consecutive stories, excluding multi-part stories and flashbacks. The first time was Frontier in Space and Planet of the Daleks. However, Planet is a continuation of Frontier and both deal with parts of the same Dalek threat, whereas some time has elapsed between the events of Day and Time and they both involve two separate Dalek threats: the Time War and the New Dalek Paradigm respectively.
 * Though considering himself not much of a "weepy guy", during the table read-through for the script of The Time of the Doctor, Matt Smith had an emotional breakdown while trying to read his final lines - specifically "I will always remember when the Doctor was me" - and cried. Steven Moffat immediately came over to his seat and hugged him while Jenna Coleman tried to avoid being overcome with sadness herself.
 * The music that plays out Matt Smith's regeneration scene is a Series 7 music track composed by Murray Gold, "Infinite Potential", which is a solemn version of "The Long Song" heard in The Rings of Akhaten. It is followed by a sampling of the Series 6 track "My Silence" as he removes his bow-tie.
 * Untranslated, the message echoing from Trenzalore is a sequence of three electronic, ringing beeps- two beeps in a row, followed by one more beep. These can be interpreted as the syllables used to pronounce the words "Doctor who?", its translation.
 * The Doctor being given a new regeneration cycle in this story narratively sets up the potential long-term continuation of the character well beyond the previously-set limit of twelve regenerations.
 * This story was promoted as the 800th episode of Doctor Who. In terms of individual installments, the actual total is higher, but a poster included with Doctor Who Magazine #468 specifies that this total does not include minisodes or prequels.
 * The Doctor's final speech before regenerating can be describe as one of the true themes of Doctor Who.
 * The hallucination of young Amelia Pond was played by an unknown child actress and not played by Caitlin Blackwood, who had played young Amelia in previous episodes, as Blackwood had aged into a teenager by the time of the episode's filming and the Doctor's hallucination was of the young Amelia as she had appeared in The Eleventh Hour. To disguise the fact that it was a different actress, young Amelia's face was obscured by drawings.
 * The poem The Eleventh Doctor receives from Clara's Christmas cracker states "Eleven's hour is over, now it's time for Twelve's" which references The Eleventh Doctor's first full story, TV: The Eleventh Hour.

Ratings
8.3 million overnight.

11.14 million according to the Broadcasters' Audience Research Board. The number includes those who recorded it and watched it within seven days.

1.9 million on BBC iPlayer the week after transmission.

Filming locations
to be added

Rumours

 * Because of the leg injury suffered by Matt Smith during filming, the Doctor would lose a leg during the episode. This proved to be false. The middle-aged and elderly versions of the Doctor, however, both rely on a walking stick to get around.  In addition, while in the TARDIS waiting for his regeneration to kick in, the youthful Doctor is mostly standing still (presumably to allow Smith to cope better), and when he walks to the console to operate he is clearly limping and in pain.
 * On 20th December, the Daily Star tabloid published the spoiler that a "fan favourite" character would appear in the episode during the regeneration. This led to several days of speculation as to who it might be before it was revealed that Amy Pond was the returning character.

Production errors

 * When the Doctor and Clara arrive at the Papal Mainframe, the right column of the TARDIS is noticeably missing.
 * When the Doctor is on the Dalek ship at the beginning of the episode, one of the Daleks' eyestalk lights are not turned on.
 * The Doctor's hairstyle changes between Amy's hallucinatory farewell and the Doctor reaching out into thin air.
 * After his regeneration, the Twelfth Doctor's first line is "Kidneys! I've got new kidneys! I don't like the colour...". He stumbles back against the TARDIS console as he cries out "Kidneys! I've got new kidneys!". In the next shot, however, as he says "I don't like the colour...", he is standing to the left of the console (as seen by the viewer).

Continuity

 * The Doctor tricks Clara into returning home in the TARDIS, presumably using Emergency Program One, although modified in that the TARDIS was programmed to return to him after Clara's departure. The Ninth Doctor previously tricked Rose into returning home in the TARDIS. Just like Clara, she managed to return both herself and the TARDIS to the Doctor, and playeda part in saving the Doctor and activating his next regeneration. (TV: The Parting of the Ways).
 * Handles' response "Affirmative" is reminiscent of K9 (TV: The Invisible Enemy, onward)
 * The Doctor begs Clara to learn to use iPlayer, suggesting her implanted hacking skills don't extend to other everyday technology (or have since worn off). (TV: The Bells of Saint John).
 * Clara's poor cooking skills are again in evidence, as she needs the Doctor's help to cook her family's Christmas turkey. (TV: Asylum of the Daleks, The Name of the Doctor).
 * The Doctor explains the Cracks in time and the events of the reboot of the Universe to Clara. (TV: The Big Bang)
 * To allow translation of the message, the Doctor uses a Seal of the High Council of Gallifrey, claiming he "nicked it off the Master in the Death Zone." The Third Doctor did exactly that, incorrectly assuming that the Master had himself stolen it. The Doctor stated at that time he would return it to the High Council at the "first opportunity". (TV: The Five Doctors)
 * The Doctor confirms to Clara that although he is "the Eleventh Doctor", he has in fact used all twelve of his regenerations, and is therefore unable to regenerate again. The two "missing" lives are the War Doctor (who was not generally referred to as the Doctor due to his actions in the Time War, and had in fact rejected the title), (TV: The Day of the Doctor) and the abortive regeneration by the Tenth Doctor when he sent his regenerative energy into a matching bio-receptacle (his severed hand) rather than change. (TV: Journey's End) The Doctor's statement also implies that River Song's sacrifice of her remaining regenerations to save his life only transferred the healing effect of regenerative energy, not her remaining lives. (TV: Let's Kill Hitler)
 * It is again confirmed that Time Lords can only regenerate twelve times, for a total of thirteen lives (TV: The Deadly Assassin, et. al.), but that a Time Lord can be granted a new regeneration cycle. The Master had been offered a new regeneration cycle by the High Council to persuade him to rescue the various Doctors trapped in the Death Zone, (TV: The Five Doctors) and was apparently given one when he was resurrected to fight in the Time War. (TV: The Sound of Drums)
 * Regenerative energy again proves to be damaging to non-organic objects, with the Doctor using some excess energy to blast the Daleks and their ship. When the Tenth Doctor regenerated, some of that energy hit the TARDIS console, causing major damage and sending it out of control. (TV: The End of Time, Part Two)
 * The Doctor visibly ages during the three hundred years between when he sends Clara home and when she returns, gaining grey hair and wrinkles and requiring a cane to walk. He ages even further during an undefined period - likely several more centuries - between when he sends Clara home again and when Tasha Lem collects her to say goodbye to him. Previously, the Doctor spent 200 years running from his fate at Lake Silencio, yet was young enough in his body to not appear to age much. (TV: The Impossible Astronaut)
 * Like the Tenth Doctor, whose visible injuries were healed as the regeneration process began, the Eleventh Doctor undergoes a pre-regenerative "reset" to his original youthful self. (TV: The End of Time, Part Two) This is the first time the Doctor has been explicitly seen to "de-age" prior to undergoing full regeneration; his comments about the reset indicates this to be uncommon.
 * It is learned that Madame Kovarian led a rogue faction of the 'Church of Silence' that broke off and travelled back along the Doctor's timeline, trying to stop him from reaching Trenzalore and answering the First Question. Their actions failed, and in fact caused the events they feared to occur; trying to blow the TARDIS up caused the cracks to appear, and the assassin they manufactured to kill the Doctor - River Song - ended up being the Doctor's wife and ally. The Doctor called this the Destiny Trap - "You can't change history if you're already a part of it."
 * A similar such paradox is set up during Day of the Daleks - the guerillas' assassination of Styles in the belief his death would prevent the Daleks' invasion of Earth actually led directly to it.
 * The Silents are revealed to be high ranking Confessional Priests of the Papal Mainframe (later the Church of Silence), which were genetically engineered to allow people to confess their sins without remembering doing so, accomplished by fashioning the priests so anyone looking at them would forget their encounter when they looked away.
 * As the Eighth, War, Ninth and Tenth Doctors did, the Eleventh Doctor examines his glowing hands before he regenerates. (TV: The Night of the Doctor, The Day of the Doctor, The Parting of the Ways, The Stolen Earth, The End of Time)
 * The Doctor silently materializes the TARDIS on Trenzalore. (TV: The Dalek Invasion of Earth, The Time of Angels, The Impossible Astronaut, et. al.)
 * The greatest fear in the Doctor's room from The God Complex is revealed to have been a crack in time.
 * The Doctor again uses the phone on the outside of the TARDIS. (TV: The Bells of Saint John, The Day of the Doctor) It had previously not been a real phone (TV: The Empty Child). He says he keeps forgetting to patch it back through the phone on the console. (TV: World War Three, The Beast Below)
 * Clara now has her own TARDIS key. (TV: The Rings of Akhaten, Hide)
 * The Doctor uses "reverse the polarity" once more (TV: The Day of the Doctor), a favourite phrase of the Third Doctor.
 * The Daleks now once again remember the Doctor (TV: Asylum of the Daleks) due to harvesting the information from Tasha Lem's mind.
 * Dalek puppets reappear. (TV: Asylum of the Daleks) Tasha Lem is able to resist her conditioning and fire on three Daleks in a way that mirrors Jenibeth Blakely.(PROSE: The Dalek Generation)
 * The Doctor eats fish fingers and custard one last time before regenerating. (TV: The Eleventh Hour, The Power of Three)
 * The Twelfth Doctor's first words — "Kidneys! I've got new kidneys!" — keep to the recent "tradition" of new Doctors immediately commenting on their bodies. Previously, the Tenth Doctor commented on his "new teeth", (TV: The Parting of the Ways) and the Eleventh on his legs. (TV: The End of Time) Past Doctors had similar comments later on. (TV: Spearhead from Space, Robot, Doctor Who, Rose)
 * The most lucid and frequent voice emanating from the crack in time is that of the General seen in The Day of the Doctor.
 * While regenerating, the Doctor hallucinates seeing his past companion Amelia Pond as both a child and an adult, similar to the Fourth and Fifth Doctors thinking of their past companions at the time of their respective regenerations. (TV: Logopolis, The Caves of Androzani)
 * While the species themselves are not mentioned, Judoon rockets (TV: Smith and Jones, The Pandorica Opens) and Silurian Arks (TV: Dinosaurs on a Spaceship) can be seen among the fleets orbiting Trenzalore at the beginning. Terileptils (TV: The Visitation) and Slitheen (TV: Aliens of London/World War Three, Boom Town) are also listed among the species present.
 * While the Doctor is protecting Christmas, a Weeping Angel is seen next to a mirror upon which "Love from the Doctor" is written. (TV: Blink)
 * This is not the first time someone rode through the Time Vortex on the outside of the TARDIS. This was previously done by Captain Jack Harkness (TV: Utopia) and the Doctor himself (TV: Hide). Clara survives the trip due to the TARDIS shielding her; Jack, who frightened the TARDIS his unnatural immortality and ability to resurrect, was not shielded and, therefore, "died".
 * The town of Christmas has a small graveyard with headstones identical to those in the mass grave from Trenzalore's alternate future. (TV: The Name of the Doctor)
 * This is the first time in the revived series to acknowledge the fact the Time Lords have a limited capacity to regenerate twelve times. The Eleventh Doctor previously joked to Clyde Langer that he could regenerate 507 times - but if you add 5, 0 and 7 together, it adds to 12, suggesting he was making a subtle hint he was near the end of his normal lifespan. (TV: Death of the Doctor)
 * The Doctor teaches the children of Christmas to do the "drunk giraffe" dance he performed at the wedding of Amy Pond and Rory Williams. (TV: The Big Bang)
 * At his oldest before the regeneration process, the Doctor's hairstyle resembles that of his first incarnation. He also carries a walking stick like his earliest incarnation did.
 * The gathering of spaceships at Trenzalore is reminiscent of the Alliance which came to Earth in 102 AD for the Pandorica. In both cases, Daleks, Cybermen, Judoon, Silurians, Sontarans, Slitheen and Terileptils were part of the gathering. The Weeping Angels are the only race seen or mentioned here not known to have been in the Alliance. (TV: The Pandorica Opens)
 * The sonic screwdriver still doesn't do wood. (TV: Silence in the Library, The Doctor, the Widow and the Wardrobe) This episode also shows that it doesn't do turkey either.
 * During his time on Trenzalore, the Doctor says "Christmas is protected" (TV: The Christmas Invasion, The Eleventh Hour) and that "cool is not cool," adding to the many things he says are not cool.
 * The puppet show put on display for the children of Christmas shows an adventure between the Doctor and a Monoid, an alien species last seen by the First Doctor. (TV: The Ark)
 * The Time Lords' contribution to the Doctor's regeneration can be considered a reversal of their reasons for forcing his regeneration from the Second Doctor to the Third Doctor as part of his punishment for multiple breaches of the First Law of Time. (TV: The War Games)
 * The Doctor says "Geronimo!" with the children of Christmas, the last instance he uses that word in this incarnation. (TV: The End of Time, Part Two onward)
 * The Heart of the TARDIS can now be easily opened up from a hexagonal panel beneath the main console unit. It was previously very difficult to access due to the risk of exposing oneself to the Time Vortex. (TV: Boom Town, The Parting of the Ways)
 * The Doctor still has a powerful dislike for wine, shown when he immediately spits out his wine back into its glass after sampling the drink that Tasha Lem courteously offers him. (TV: The Lodger, The Impossible Astronaut)
 * The Doctor fixes a little girl's broken toy train while staying at Christmas, but goes too far and bends to his desire to add modifications, such as anti-gravity flight mechanisms. He previously overhauled the Digby Estate with various unnecessary contraptions to impress Madge Arwell's children. (TV: The Doctor, the Widow and the Wardrobe) Going back to his previous incarnation, he made a DNA detector that was supposed to go "ding" in the presence of a Zygon, but didn't know when to stop himself, giving it the ability to microwave frozen dinners from up to twenty feet and download comics from the future. (TV: The Day of the Doctor)
 * The aged Doctor taps his nose, much like the Curator and the Fourth Doctor did. (TV: The Day of the Doctor)
 * Some of Amy's drawings reveal monsters seen in previous episodes, including the Saturnyne (TV: Vampires of Venice), Peg Dolls (TV: Night Terrors) and the new Daleks (TV: Victory of the Daleks)
 * Avoiding the use of time travel, if Kovarian used Demons Run as a base contemporaneously with the Siege of Trenzalore, then this story may begin before and end after the 52nd century as the Battle of Demons Run takes place then. (TV: A Good Man Goes to War)
 * Clara does not recognize the name Amelia, even though the TARDIS once displayed an image of her (TV: Clara and the TARDIS).
 * The Doctor is shown in an "in-between" stage of his regeneration, with his youthful appearance briefly restored. This is described as a "reset" prior to the Doctor's new regeneration cycle starting. The Tenth Doctor experienced a similar restoration and delay, mainly because he resisted the final change until he couldn't contain the build-up of regenerative energy any more. (TV: The End of Time) A possibly similar (but never-explained) apparition, the Watcher, was seen when the Fourth Doctor regenerated. (TV: Logopolis)
 * The Doctor forgetting how to fly the TARDIS isn't the first time The Doctor has had a memory related mishap after regenerating; most of his incarnations experienced some small, short-term memory loss and/or personality confusion immediately following regeneration. The Eighth Doctor in particular forgot who he was until much later when the Eye of Harmony was opened. (TV: Doctor Who)
 * Prisoner Zero's statement "Silence will fall" was what started the great mystery of the Silence. Since then all the adventures The Doctor has had from then to arriving to Trenzelore have been shaped by the Silence. Having learned what the Silence truly were, all remaining question referring to them answered, and having averted the future they feared would come to past, the Doctor's regeneration signifies the end of the mystery.
 * Similar to how the Doctor kept Handles, a non-sentient robot, alongside him as company on Trenzalore for 300 years, an alternate version of Amy Pond who had grown 36 years older when she became trapped in the Two Streams Facility converted a non-sentient Handbot into the likeness of her husband to keep her company. (TV: The Girl Who Waited)

Home video releases
The Time of the Doctor was released on Region 2 DVD, and Region B 3D Blu-ray on 20 January 2014. The other Eleventh Doctor Christmas specials, A Christmas Carol, The Doctor, the Widow and the Wardrobe and The Snowmen, were also included on both versions.