The Doctor's death

Much like their origin, the Doctor's death was a matter of conflicting accounts and alternate timelines. (PROSE: Alien Bodies, TV: The Impossible Astronaut, The Name of the Doctor)

The Doctor's mortality
Through their ability to regenerate, the Doctor was able to "cheat death" on numerous occasions. (TV: The Tenth Planet, The Parting of the Ways) However, the Tenth Doctor noted that he could be killed without allowing for regeneration. (TV: The End of Time) As such, the Doctor was not truly immortal, which the Fifth Doctor deemed impossible even for a Time Lord. (TV: The Five Doctors) Even allowing for regeneration, the Tenth Doctor regarded the change it entailed as a form of death. (TV: The End of Time)

Impact on the universe
Due to their impact on the universe, having "touched so many lives" and "saved so many people", the prospect of the Doctor's death would affect a great many people. Indeed, from an alternate reality in which River Song refused to kill the Doctor, news that the Doctor was dying led millions, all across time and space, to offer their help. (TV: The Wedding of River Song) At the same time, Vislor Turlough, companion to the Fifth Doctor, noted that the Doctor had many enemies who would delight in his death, an observation which Kamelion concurred with. (TV: The Caves of Androzani) However, even once remarked that "a cosmos without the Doctor scarcely bears thinking about." (TV: The Five Doctors) Multiple occasions in which the Doctor was killed prematurely resulted in stars burning out across the universe. (AUDIO: The Furies, TV: Turn Left, The Name of the Doctor)

The Twelfth Doctor himself, after spending some time resisting regenerating even it if meant his final death, ultimately conceded to the TARDIS that the "silly old universe" still needed saving and that "[they'd] get it all wrong without [them]." (TV: Twice Upon a Time)

In a dissenting account of the Doctor's lives following the Eighth Doctor, what appeared to be the final death of the Twelfth Doctor led the Master and a shipful of Daleks, who were saved when the Doctor stopped their Zectronic Beam Controller from imploding, to openly renounce their evil ways. (TV: The Curse of Fatal Death)

Denial and regret
After the Twelfth Doctor's apparent death, Bill Potts told him she'd never believe he was really dead, because "one day everyone's just going to need [him] too much." She brought him into the TARDIS, as "the only place he'd rest in peace", if he could do that anywhere. (TV: The Doctor Falls)

After the Eleventh Doctor's supposed death at Lake Silencio, Amy Pond needed desperately to talk with him to understand what happened. When River Song visited, Amy solemnly noted she was still having adventures with a younger Doctor, running around with him, while for Amy, the Doctor was already dead. Amy was gleeful when she found out that he'd survived. (TV: The Wedding of River Song)

A feeling inside the heart
Before encountering the Tenth Doctor, Sarah Jane Smith believed that the Doctor had died, having left her for so long without returning. (TV: School Reunion) However, by another account, Sarah Jane always believed that when the Doctor died, she would know, because she would feel it. Jo Jones believed the same thing, having travelled with the Third Doctor:

When the Shansheeth brought news of the Doctor's supposed death, Sarah knew he was still alive, and proclaimed that she would find him. Rani Chandra thought of all the lives he'd touched on Earth, and was saddened that the whole world wasn't mourning. The Eleventh Doctor later reunited with Sarah Jane and Jo, putting these claims to rest. (TV: Death of the Doctor)

Close encounters
Before regenerating, the Fifth Doctor said it seemed "different this time", and worried that he might actually die from the spectrox toxaemia. However, visions of his companions urged him to go on. 's assertion that he must die stirred the Doctor to finally regenerate. (TV: The Caves of Androzani)

Similarly, the Twelfth Doctor's delayed regeneration on board a Mondasian colony ship caused Bill Potts to believe he died. Bill and Heather brought him into the TARDIS, and the Twelfth Doctor had visions of past companions saying his name. On hearing 's voice, he awoke and began the process, (TV: The Doctor Falls) though it took an encounter with the First Doctor to convince him to finally allow himself to change. (TV: Twice Upon a Time)

According to another account, a Twelfth Doctor believed that exposure to a zectronic beam had destroyed his ability to regenerate, anticipating his final death. However, in a feat which the Master deemed to be impossible, he nevertheless regenerated into the Thirteenth Doctor, with Emma supposing that "maybe even the universe can't bear to be without the Doctor." (TV: The Curse of Fatal Death)

Complete death
The Eighth Doctor was unique amongst his other incarnations in that he was technically dead both when he regenerated from the Seventh Doctor and when he regenerated into his successor incarnation. Following a non-fatal shooting, the Seventh Doctor was taken to a San Francisco hospital, where subsequent exploratory surgery by Grace Holloway with a camera accidentally clogged a vein; the anaesthetic he had been given delayed regeneration for several hours and almost destroyed the process. (TV: Doctor Who) The Eighth Doctor himself died aboard Cass Fermazzi's gunship when it crash-landed on Karn, but was resurrected for four minutes by the Sisterhood of Karn, enabling him to regenerate into the War Doctor. (TV: The Night of the Doctor)

War in Heaven
By one account, the Doctor died during the War in Heaven. His body became known as "the Relic", which contained all the Doctor's knowledge. It was contained within a glowing metal box with two Greek letters on it, and was planted in a bunker beneath the ruins of Smithmanstown on Dronid, where it was found by the Corporation. (PROSE: Alien Bodies)

Bernice Summerfield tried and failed to locate the Doctor's remains, finding only empty graves. (PROSE: The Shape of the Hole) The Eighth Doctor later destroyed the Relic inside his TARDIS, having found it at an auction in the Unthinkable City. (PROSE: Alien Bodies)

Lake Silencio
It was a matter of historical record that the Eleventh Doctor was killed at Lake Silencio, Utah on the planet Earth at 5:02 PM on 22 April 2011 at the hands of River Song, born Melody Pond. Knowing this, the crew of the Teselecta, a ship of the Justice Department which operated to inflict "hell" on unpunished criminals, deviated from their mission to punish Adolf Hitler when they discovered River. It was through this encounter that a younger version of the Eleventh Doctor became aware of his recorded death. (TV: Let's Kill Hitler)

Though at first the Doctor was willing to accept his coming death, (TV: Closing Time) he later found a way around this fixed point in time by asking the Teselecta crew for help. To preserve history, the Teselecta took on the form of the Eleventh Doctor, taking his place in the events to follow. (TV: The Wedding of River Song) River Song was procured by the Kovarian Chapter of the Silence, and placed in a space suit beneath Lake Silencio, (TV: Closing Time) where she would be made to shoot the Doctor, causing a brief regeneration before cutting this short with her second blast. (TV: The Impossible Astronaut)

River Song's World
In a new timeline, River Song refused to play her part, creating an unstable alternate reality in which all of Earth's history took place at once. On discovering that the Eleventh Doctor was safe on board the Teselecta, however, during her wedding with the Doctor, River initiated contact with him again, allowing time to continue, as it had before. (TV: The Wedding of River Song) Afterwards, River Song was imprisoned at the Stormcage Containment Facility, on charges of murder, (TV: Flesh and Stone) for having "killed" the Doctor. (TV: The Wedding of River Song) She went on many adventures with the Doctor during her imprisonment, (HOMEVID: First Night, Last Night) and became known for escaping, (AUDIO: The Bekdel Test) though she always returned in the end, to serve her sentence. (TV: A Good Man Goes to War) During an adventure with a younger Doctor, River refused to reveal the name of the man she'd killed. (TV: Flesh and Stone)

River Song was later released, since it seemed the man she killed had never existed, when the Eleventh Doctor expunged his name from all records. (TV: The Angels Take Manhattan)

Original timeline
In one timeline, (TV: The Time of the Doctor) the Eleventh Doctor died on Trenzalore in a great battle. He was buried inside his TARDIS, which grew to an enormous size due to size leakage, acting as his tomb. As the Eleventh Doctor explained, the TARDIS was dying as well.

In a confrontation with the Doctor and Clara Oswald, the Great Intelligence entered the Doctor's time stream in the Doctor's tomb, which he used to attack his entire timeline, turning all his victories into defeats. As a result, the Doctor was, as Vastra put it, "dying all at once", including as the Fifth Doctor on Androzani and as the Eleventh Doctor in the Dalek Asylum. These deaths were averted when Clara herself entered the time stream, splintering herself into echoes who saved the Doctor, across all known incarnations. (TV: The Name of the Doctor)

New timeline
Later on, Clara Oswald helped create a new timeline by convincing the Time Lords to grant the Doctor a new regeneration cycle, allowing him to regenerate on Trenzalore. Back in his TARDIS, the Eleventh Doctor regenerated into the Twelfth Doctor. (TV: The Time of the Doctor)

Alternate realities
In an alternate timeline created by using the Chronovore Artemis, (PROSE: No Future) the Third Doctor was killed by Morka during his confrontation with the Silurians, resulting in humanity being decimated as the Silurians attempted to return Earth to its original state. (PROSE: Blood Heat)

As the Lord of the Manor, a future version of the Fifth Doctor who had lived somewhere between 100,000 and a million years, ruling over Stockbridge, the Doctor finally died when the original Doctor collapsed the time bubble in which the town had been contained. (AUDIO: The Eternal Summer)

When Rose Tyler changed history by saving the life of her father, Pete Tyler, Reapers appeared and consumed the Ninth Doctor as he tried to protect his human company. Exclaiming that the Doctor was dead, Rose blamed herself. However, Pete gave his life to stop the Reapers by stepping in front of the car that killed him, resulting in the return of the Doctor along with everyone else the Reapers had consumed. (TV: Father's Day)

Donna's World
Donna's World was a parallel universe created when a fortune teller fitted a Time Beetle of the Trickster's Brigade to Donna Noble, companion of the Tenth Doctor, changing her past so that on one day she turned right rather than left. The ensuing chain of events meant that she never met the Doctor and so was not there to stop him when he drowned the Racnoss, resulting in him dying with them before he could regenerate, his body being retrieved by UNIT along with the TARDIS. In the following years, the Earth was devastated by alien invasions which the Doctor would have stopped. Allies of the Doctor, both those he had met and those he would have met, opposed these incursions in his stead but most of them were killed. Eventually, the stars themselves began to go out, a result of the reality bomb. Rose Tyler, a former companion who returned from Pete's World, came to Donna and saw that she was sent back in time using what remained of the TARDIS, which she believed to be dying. Donna herself gave her life so that her past self would be forced to turn left, thus correcting history. (TV: Turn Left)

Other universes and dimensions
In one parallel universe, Ruth Mills knew about the Doctor's regeneration limit. She forced him to regenerate into a new incarnation, then killed him too, musing about how many times she'd have to do this before the Doctor was dead. (AUDIO: Full Fathom Five)

Duplicates
The Eleventh Doctor's Ganger sacrificed himself and Ganger Miranda to stop Ganger Jennifer, setting the sonic screwdriver to a frequency that would cause the Flesh to collapse, in full knowledge that this would destroy him too so that the others would be encouraged to negotiate better conditions for the Gangers. (TV: The Almost People)

Meta-narrative
Many commentators have pointed out that regeneration was introduced to recast William Hartnell because if the Doctor ever died, "the show would end." This was what Steven Moffat has called "a clever way to solve a staffing problem". This narrative technique is what has allowed the character of the Doctor to survive through 60 years of television history, shaking up the core dynamic of the series each time a new lead actor is cast, rather than ending when the core cast has left, as many other series do.

However, this same problem has caused problems for. For example, TV: The Impossible Astronaut sets up the expectation that the Eleventh Doctor will die in the series finale. Though this left fans speculating about how the Doctor will evade death this time — with theories ranging from "the Doctor used his Ganger" to "the Doctor we've been following is the Ganger" — the weight of the Doctor's true, final end would act on no one, because, to anyone engaging with the material, the Doctor's death could only spell one thing: the end of the programme.

Sensationalism
The Doctor's death was teased by the title of the fifth episode of The Chase, "The Death of Doctor Who", which ultimately referred to the destruction of the First Doctor's robotic duplicate. Years later, the Eleventh Doctor made his appearance in The Sarah Jane Adventures story Death of the Doctor, which featured his staged funeral.

Regeneration limit
The 1976 serial TV: The Deadly Assassin set a challenge in establishing that Time Lord have a regeneration limit of 13 incarnations. The Valeyard would later be introduced in TV: The Mysterious Planet as a manifestation of the Doctor from "between his twelfth and final incarnations." Some readers have determined, as a result, that the final Doctor seen in PROSE: Alien Bodies would be the Thirteenth Doctor, having used up his incarnations by the time of the War.

Eventually, Steven Moffat decided to write his way out of the regeneration limit by having the Time Lords grant the Doctor a new regeneration cycle in TV: The Time of the Doctor, in order to allow the franchise to continue without breaking continuity with earlier Doctor Who serials, which he respected.

Non-narrative sources
The final objective of the online video game NOTVALID: The Last Dalek was for the player-controlled Dalek to exterminate the Ninth Doctor and destroy the TARDIS.