The Fourth Doctor has a precognitive vision about the President of the Time Lords being assassinated. The Doctor goes to Gallifrey to stop the assassination. At the Panopticon, a Gallifreyan ceremonial chamber, he notes a camera stationed on an unguarded catwalk. He also spots a sniper rifle next to the camera. The Doctor fights his way to the catwalk, warning that the President is about to be killed. Unbeknownst to the Doctor, the assassin is among the delegates and shoots the President dead. However, the crowd sees the Doctor on the catwalk with the rifle and assumes he is the killer.

Under interrogation, the Doctor maintains that he has been framed. Eventually, Castellan Spandrell starts to believe him and orders Engin to assist him in an independent investigation. To delay his possible execution, the Doctor invokes Article 17 and announces that he will run for President, which guarantees liberty for those running for office during the course of an election.

The Doctor realises that it was the Master who had sent him the premonition of the assassination through the Matrix, a vast electronic neural network which can turn thought patterns into virtual reality. He decides to enter the Matrix to track the Master. In the Matrix, the Doctor confronts an assassin who eventually reveals himself as Chancellor Goth. The Master, realising that Goth has been effectively defeated, tries to trap the Doctor in the Matrix by overloading the neuron fields. Engin gets the Doctor out of the Matrix, but Goth is fatally burnt.

The Doctor and Spandrell, accompanied by soldiers, make their way to the chamber where the Master and Goth were accessing the Matrix. They find the Master without a pulse and Goth dying. Goth reveals that he found the Master, near death, on Tersurus. The Master was nearing the end of his final regeneration. Goth went along with his schemes mainly for power: he knew the President had no intention of naming him as a successor, but if a new election were held, Goth would be the front-runner. Before he dies, Goth warns that the Master has a doomsday plan.

Attempting to piece together what the Master and Goth were planning, the Doctor inquires as to what becoming the President entails. He is told that the President has access to the symbols of office: the Sash and Great Key of Rassilon. As Engin plays records that describe how Rassilon found the Eye of Harmony within the "black void," the Doctor realises these objects are not merely ceremonial. He also realises that the Master injected himself with a neural inhibitor that mimics a deathlike state and is still alive.

The Doctor, Spandrell, and Engin arrive at the morgue to find that the Master has revived. The Master seizes the Sash from the President's corpse and traps the three in the morgue. The Doctor explains that the Eye is actually the nucleus of a black hole, an inexhaustible energy source that Rassilon captured to power Gallifrey; the Sash and Key are its control devices. The Doctor deduces that the Master was planning to steal this energy to gain a new cycle of regenerations; however, if the Eye is disrupted, Gallifrey will be destroyed and a hundred other worlds will be consumed in a chain reaction.

Inside the Panopticon, the Master makes his way to the obelisk containing the Eye. He unhooks the coils that connect it to Gallifrey and is prepared to access the energy. The Doctor makes his way to the Panopticon via a service shaft. The Citadel begins to quake, and cracks appear in the floor. The Doctor and the Master fight, until the Master loses his footing and falls into a chasm. The Doctor reconnects the coils and saves Gallifrey, although half the city is in ruins and many lives have been lost.

The Doctor is now free to return to his TARDIS. He bids farewell but also warns that the Master may not be dead, as he had harvested energy from the obelisk before he was stopped and may have been able to channel it. As the Doctor's TARDIS dematerialises, Spandrell and Engin witness the Master sneak into his own TARDIS and escape.

The thirteenth incarnation of the Master was the last in his original regeneration cycle. Following an incident that resulted in his body being horribly disfigured, he began searching for a way to restore his Time Lord body, with only his intense hatred and burning anger keeping him alive.

While he would find numerous means of extending his life beyond natural limits, he would inevitably revert to his decayed thirteenth form before suffering a conclusive end at the hands of the Ravenous.

Having regenerated into his thirteenth incarnation at an accelerated rate due to living a life "more rackety than the Doctor's", (PROSE: A Brief History of Time Lords) that had constant pressure and danger, in addition to using some incarnations as disguises, (PROSE: Doctor Who and the Deadly Assassin) the Master eventually found himself trapped as a wraith-like living cadaver, "horribly emaciated", for whom "no regeneration was possible". (TV: The Deadly Assassin)

There were, however, multiple accounts of how this came about.

According to one account, the "UNIT era" Master drove his car into a wall in the mid-1970s. His charred remains were recovered by the human authorities, who identified him as the scientist Carl Thascales and declared him dead, never realising the Master's burned body still clung to life. (PROSE: Falls the Shadow)

By another account, the Decayed Master emerged as a result of Susan Foreman forcing the "UNIT era" Master out onto Tersurus and attacking him with the Tissue Compression Eliminator while he was holding the Daleks' matter transmuter, damaging him to the extent that regeneration could not repair the damage. (PROSE: Legacy of the Daleks)

According to Missy and the Thirteenth Doctor, the Master ended up in his rotting, lich-like state when he attempted to regenerate "one time too many" past the twelve-regeneration limit. (PROSE: Meet Missy!, The Doctor vs the Master)

According to yet another set of accounts, the "UNIT era" Master began to regenerate after being injured in a temporal storm after an encounter with the Twelfth Doctor. Prior to his regeneration, his body was beginning to decay, yet he declared himself the master of life itself and attempted to regenerate to survive. (COMIC: Doorway to Hell) Because he was suffering from an artron energy deficiency (PROSE: The Dead Travel Fast) as a result of the storm, his regeneration went wrong (COMIC: Doorway to Hell) and his new incarnation was brought into existence already horribly scarred. (PROSE: The Dead Travel Fast)

Yet another account showed that the Thirteenth Master, as distinct from the "UNIT era" version, had enjoyed some span of existence in un-disfigured form before being injured in events involving his own future self. 

Doctor Who first appeared on BBC TV at 17:16:20 GMT on Saturday, 23 November 1963; this was eighty seconds later than the scheduled programme time, because of the assassination of John F. Kennedy the previous day.[5][6] It was to be a regular weekly programme, each episode 25 minutes of transmission length. Discussions and plans for the programme had been in progress for a year. The head of drama Sydney Newman was mainly responsible for developing the programme, with the first format document for the series being written by Newman along with the head of the script department (later head of serials) Donald Wilson and staff writer C. E. Webber. Writer Anthony Coburn, story editor David Whitaker and initial producer Verity Lambert also heavily contributed to the development of the series.

The programme was originally intended to appeal to a family audience[8] as an educational programme using time travel as a means to explore scientific ideas and famous moments in history. On 31 July 1963, Whitaker commissioned Terry Nation to write a story under the title The Mutants. As originally written, the Daleks and Thals were the victims of an alien neutron bomb attack but Nation later dropped the aliens and made the Daleks the aggressors. When the script was presented to Newman and Wilson it was immediately rejected as the programme was not permitted to contain any "bug-eyed monsters". According to producer Verity Lambert; "We didn't have a lot of choice — we only had the Dalek serial to go ... We had a bit of a crisis of confidence because Donald [Wilson] was so adamant that we shouldn't make it. Had we had anything else ready we would have made that." Nation's script became the second Doctor Who serial – The Daleks (also known as The Mutants). The serial introduced the eponymous aliens that would become the series' most popular monsters, and was responsible for the BBC's first merchandising boom.

The BBC drama department's serials division produced the programme for 26 seasons, broadcast on BBC 1. Due to his increasingly poor health, the first actor to play the Doctor, William Hartnell, was replaced by the younger Patrick Troughton in 1966. In 1970 Jon Pertwee replaced Troughton and the series at that point moved from black and white to colour. In 1974 Tom Baker was cast as the Doctor. His eccentric style of dress and quirky personality became hugely popular, with viewing figures for the show returning to a level not seen since the height of "Dalekmania" a decade earlier. In 1981, after a record seven years in the role, Baker was replaced by Peter Davison, at 29 by far the youngest actor to be cast as the character in the series' first run, and in 1984 Colin Baker replaced Davison. In 1985 the channel's controller Michael Grade attempted to cancel the series, but this became an 18-month hiatus instead. He also had Colin Baker removed from the starring role in 1986. The role was recast with Sylvester McCoy, but falling viewing numbers, a decline in the public perception of the show and a less-prominent transmission slot saw production ended in 1989 by Peter Cregeen, the BBC's new head of series. Although it was effectively cancelled with the decision not to commission a planned 27th season, which would have been broadcast in 1990, the BBC repeatedly affirmed, over several years, that the series would return.

While in-house production had ceased, the BBC hoped to find an independent production company to relaunch the show. Philip Segal, a British expatriate who worked for Columbia Pictures' television arm in the United States, had approached the BBC about such a venture as early as July 1989, while the 26th season was still in production. Segal's negotiations eventually led to a Doctor Who television film, broadcast on the Fox Network in 1996 as an international co-production between Fox, Universal Pictures, the BBC and BBC Worldwide. Starring Paul McGann as the Doctor, the film was successful in the UK (with 9.1 million viewers), but was less so in the United States and did not lead to a series.

Licensed media such as novels and audio plays provided new stories, but as a television programme Doctor Who remained dormant until 2003. In September of that year, BBC Television announced the in-house production of a new series after several years of attempts by BBC Worldwide to find backing for a feature film version. The executive producers of the new incarnation of the series were writer Russell T Davies and BBC Cymru Wales head of drama Julie Gardner.

Starring Christopher Eccleston as the Doctor, Doctor Who finally returned with the episode "Rose" on BBC One on 26 March 2005. Eccleston left after one series and was replaced by David Tennant. There have since been eleven further series in 2006–2008, 2010–2015, 2017–2018, 2020, and Christmas/New Year's Day specials every year since 2005, with the exception of 2018. No full series was broadcast in 2009, although four additional specials starring Tennant were made. Davies left the show in 2010 after the end of series 4 and the David Tennant specials were completed. Steven Moffat, a writer under Davies, was announced as his successor, along with Matt Smith as the new Doctor. Smith decided to leave the role of the Doctor in the 50th anniversary year. He was replaced by Peter Capaldi.

In January 2016, Moffat announced that he would step down after the 2017 finale, to be replaced by Chris Chibnall in 2018. The tenth series debuted in April 2017, with a Christmas special preceding it in 2016. Jodie Whittaker was announced as the first female Doctor, and has appeared in two series and is scheduled to reprise her role in a third, shorter series. 

The 2005 version of Doctor Who is a direct plot continuation of the original 1963–1989 series and the 1996 telefilm. This is similar to the 1988 continuation of Mission Impossible, but differs from most other series relaunches which have either been reboots (for example, Battlestar Galactica and Bionic Woman) or set in the same universe as the original but in a different time period and with different characters (for example, Star Trek: The Next Generation and spin-offs).