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)
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)
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 the Tremas Master 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)
Impact on companions
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)
Death and regeneration
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. The Tremas Master'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 Missy'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)
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 found away around this fixed point in time by asking the Teselecta crew for help. 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 this would be cut short by a second shot. (TV: The Impossible Astronaut)
River Song's World
In one timeline, River Song refused to play her part, creating an alternate reality in which all of Earth's history took place at once. However, discovering that the Eleventh Doctor was safe on board the Teselecta, during her wedding with the Doctor, River initiated contact with him again, allowing time to continue, as it had before. Afterwards, River Song was imprisoned at the Stormcage Containment Facility, on charges of murder, for having "killed" the Doctor. (TV: The Wedding of River Song) She went on numerous 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)
Trenzalore
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
As the Lord of the Manor, a future version of the Fifth Doctor who 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)
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)
Behind the scenes
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.
