The Chronicles of Doctor Who? (short story)

 was a short story written by John Leekley in 1994, outlining the life and adventures of a reimagined version of the Doctor, as narrated by his grandfather Barusa. It was intended to form the basis of a reboot of Doctor Who to be produced by Amblin Entertainment, plans which would later evolve into the 1996 Doctor Who TV Movie.

Although it was clearly incompatible with the conventional Doctor Who universe, elements of mythology introduced in this story, including the idea of the Doctor being half-human and Ulysses as the name of his Time Lord father, would go on to be introduced to mainstream Doctor Who continuity. Additionally, the Eighth Doctor comic story Fire and Brimstone, published in 1997, confirmed that the universe of The Chronicles of Doctor Who? existed as a parallel universe to mainstream Doctor Who continuity, with Daleks from this world making their way into the Eighth Doctor's and making war with the surviving "classic" Daleks.

The Chronicles of Doctor Who? was not originally intended for a full commercial release, with only a few copies of the "Leekley Bible" being printed and distributed to producers as part of the pitch for the retooled TV series. However, long after the plans for the TV series were cancelled, the full text of The Chronicles of Doctor Who? was printed in 2000's Doctor Who: Regeneration, alongside background documentary material about its textual history and other documents related to the Leekley reboot.

Publisher's summary
I AM CARDINAL BARUSA… TIME LORD OF GALLIFREY.

This is my official insignia, and my personal glyph. Having transcended the confines of body, I exist now amidst the crystals of the Domed City of Gallifrey, which resonate with their beautiful sounds… much like the wind chimes along the seas of the Blue Planet… the place you call Earth.

I have decreed that my adventures with the Doctor and his flying ship, the TARDIS, in our quest to find his father Ulysses, be written down by a scribe. I have instructed him to write these chronicles in the language of the Blue Planet, in long flowing script, because I believe that is the way the Doctor prefers it. Our own hieroglypics of Gallifrey can't capture the real adventure of it all, our glyphs are far too precise… they are meant to convey the logic of the law, and the science of time travel, which are the two proud hallmarks of Gallifrey. This odd elliptical language of the Blue Planet is far more appropriate to the Doctor, who seems to prefer humour over efficiency.

The Doctor wishes the people of the Blue Planet to know of our travels… to see for themselves that these worlds we have visited are not so distant after all. Those companions who travelled with us in our adventures can attest to this… if they will be believed by humankind…

Plot
Cardinal Barusa, residing as a disembodied spirit in the crystals of the Domed City of Gallifrey, has a scribe transcribe an account of his adventures across the universe with his grandson, the Doctor.

This story begins millennia before the Doctor's birth with the discovery by Rassilon, founder of Time Lord society, of the secrets of time travel. He creates the Matrix, a computer underneath the Domed City, which will serve as a record of all life and events in the universe, and of the memories and experiences of the Time Lords themselves. Before the TARDISes are fully developed, however, many early Time Explorers are lost, adrift in time, including Barusa's own son Ulysses.

Before his disappearance, however, Ulysses begat a son, known "in later lives" as the Master and whose sole ambition is to one day wear the Presidential Sash. His only contemporary to equal him in intellect and charisma is the Doctor, an orphan believed to be the last scion of an extinct Clan. However, the Doctor is volatile and mercurial, even at 800 years of age and with seven incarnations behind him — preferring to sneak away from Gallifrey for extended period of times and meddle in the history of the Blue Planet rather than play politics.

Skipping ahead in the timeline of his narrative, Barusa chooses to illustrate this point by inserting an entry from his own journal, relating an encounter between the Doctor and Napoléon Bonaparte shortly before the Battle of Waterloo. The interview sees Napoléon picking up on the Doctor's uncanny knowledge of military history and demanding to know more about who he is, about which the Doctor remains evasive. When the Doctor eventually walks out of Napoléon's tent at 4 in the morning, he is shaking his head, upset that Napoléon won't listen to him. He returns to the Doctor's TARDIS where Barusa, who is messing with the circuitry, criticises him yet again for not adhering by the Time Lords' traditional non-interference policy. The two quickly move on to another argument when the Doctor notices that Barusa is trying to switch the chameleon device back on in order to make the ship lose its police box appearance, which the Doctor quite likes. However, the Doctor ends up agreeing to leave this era of time and move on when Barusa reminds him they are supposed to be looking for his father.

Having finished narrating this incident, Barusa returns to "that time, so long ago, when [he] first ventured forth with the Doctor on his adventures". At this time, due to the mysterious bond which exists between the geological forces of Gallifrey and the state of mind of its people, mesas and rifts are splitting the grounds around and — increasingly — below the Domed City even as the population itself is growing divided and factional. The Master has corrupted a large number of the population with "dark dreams" of Gallifrey actively dominating all life forms in its galaxy, and already begun corrupting the "cold logic of the bureaucrats and law makers". Barusa, nearing his twelfth and final regeneration, announces in the Panopticon that he has chosen as his successor, not his grandson and rightful heir the Master, but the Doctor. Heated debate ensues between supporters of the Doctor and the Master. The Doctor himself is asked to take the stand, and delivers a heated speech denouncing the current state of Time Lord society as corrupt and decadent. This proves to have been misjudged, with the open accusations turning the crowd against him instead of galvanising progressive sentiment, and the council banishes the Doctor into the forbidden desert outside the Domed City right there and then.

The Doctor spends months traipsing through inhospitable wilderness. Without food or drink, he is reduced to voluntarily halting one of his hearts to preserve his life. Eventually, he finds himself before the Tomb of Rassilon, whose sealed entrance is carved into a huge cliff-face. He finally collapses, but is nursed back to health by the Outcasts, of whom he knew as a fearsome tribe inhabiting the wilderness, but who reveal that the are actually a secret order "fiercely devoted" to Rassilon's legacy, who guard the Tomb and its secrets. They eventually agree to show him a secret entrance to the tomb via a cave system, and the Doctor is able to unearth the mythical Scrolls of Rassilon, of which it was said that the one who found them would "lead the people of Gallifrey out of the Darkness, and prevent the planet from shattering".

Sneaking back into the Domed City, the Doctor finds Barusa on his death bed, clinging to life in an effort to delay the Master's now-inevitable rise to power. He tells Barusa about the Scrolls' content and his telepathic intuition that the key to Gallifrey's salvation lies on Earth. Barusa takes this opportunity to reveal to the Doctor the truth of his birth: he is actually also Ulysses's son, the Master's half-brother, born on the Blue Planet to a human mother (the peasant girl Annalisse) before he was smuggled to Gallifrey to be raised as a Time Lord. Finally, Barusa passes away. Meanwhile, the Time Lords, now under the Master's control, have sentenced the Doctor to total disintegration, making him a wanted man. The Doctor steals the Doctor's TARDIS just as Barusa's twelfth and final incarnation dies, with his final regeneration freeing his soul from his last body. However, much to his surprise, Barusa finds himself drawn to the Doctor and his spirit embeds itself in the Doctor's newly-acquired TARDIS even as it dematerialises, with the controls set for Earth. This is the start to their many and adventurous journeys through time and space.

Early on in these travels, the two make their way to the last space-time coordinates sent back to Gallifrey by Ulysses before the Time Lords lost contact with him for the last time. They turn out to be the Cairo Museum in Egypt, on 23 November 1994. There, the Doctor and Barusa finds a sarcophagus attributed to the pharaoh Cheops, but whose painted likeness is the very image of Ulysses. When they open it, it is empty save for a note written in Gallifreyan, from Ulysses to the Doctor: "To my son, who will search for me. Forgive me for leaving you behind. One day we will find each other again…". The Doctor is overjoyed, and ends up talking to the mummies about his life while smoking cigars.

Eventually, the Doctor's TARDIS is drawn back to Gallifrey, and the Doctor is brought before the Master and the Council; Barusa fears that the Master will have the Doctor executed. However, in a surprising reversal, the Master publicly embraces his brother and offers him amnesty in exchange for carrying out some tasks across the universe for the Time Lords' benefit. The first concerns a species of warmongering aliens called the Daleks, which have been "swarming across the far end of the Galaxy", wiping out entire species. The Master has the Doctor go back in time to their home planet of Skaro at the time of their creation, and prevent them from ever coming into existence.

Landing on Skaro, the Doctor and Barusa find the planet to be horribly irradiated, having been rendered inhospitable by a full-scale nuclear war between the peoples of its only two continents, the Kaleds and the Thals. After discovering that the seemingly benevolent Kaled scientist Davros is actually working on the creation of the Daleks, the Doctor attempts to denounce him to the Kaled High Council, only for Davros to leak the Kaled base's location to their enemies the Thal, resulting in all Kaleds save for Davros and his creations being destroyed. The Doctor later tries to sneak back into the incubator room where more Daleks are being hatched, only to be confronted by Davros, who had let him in as a trap and now wants to feed him to the Daleks. Before he can do so, a further double-cross occurs as the Master himself materialises and revealed to the Daleks how Davros betrayed their ancestors. The Daleks destroy their creator and pledge allegiance to the Master. The Doctor finally detonates the incubator room, though he cannot destroy the Master and the already-living Daleks. He considers going further back in time to undo the entire chain of events, but ultimately cannot find the strength to bear the responsibility of altering the history of the galaxy on such a massive scale: "we are not gods".

The Doctor and Barusa continue looking for Ulysses through time and space in the TARDIS, now pursued by the Daleks. They go on many adventures which Barusa relates by inserting short summaries into his chronicle — including encounters with the pirate Blackbeard in 18th century Spain — who turns out to have been Ulysses in disguise —, the war criminal Magnus Greel in 20th century New York City, the marauding cyborgs know as the Cybs, an alien who has merged with a light-house keeper in 1906, an "evil force" known as the Toymaker, the gunslinger Doc Holliday, a group of Neanderthals in Tibet, and with a colony ship where the whole population of the future Earth is frozen in cryo-stasis, only to be preyed on by parasitic insect creatures.

Eventually, the Doctor and Ulysses are reunited at last, "with great joy". They return to Gallifrey, bringing with them "all the strength and curiosity that had been lost… (…) passion and, even more importantly, compassion". With Ulysses to prove his lineage, the Doctor is allowed to replace the Master as President and wear the Sash of Rassilon. As the Time Lord population's divides heal, so do the "bottomless crevasses" that were threatening to tear Gallifrey itself apart close again. Barusa's spirit transfers itself from the crystals of the TARDIS to those of the Domed City. However, as Barusa points out, in subsequent years, the Doctor still occasionally sneaks away from his duties aboard the TARDIS to engage in further adventures, just for the fun of it.

Characters

 * The Doctor
 * Barusa
 * Rassilon
 * Ulysses
 * The Master
 * Napoléon Bonaparte
 * Annalisse
 * Davros

Worldbuilding

 * During regeneration, the Time Lord's new shape is chosen by their unconscious, "as a dream is chosen". Regenerations can be triggered by old age, mortal injury or direct order of the Time Lord Council.
 * On Gallifrey, the title of "Doctor" denotes one who has "mastered all fields of knowledge".
 * Barusa believes that the Doctor is "the only Time Lord that ever lived who was born on another planet".
 * Gallifrey has space colonies.
 * Annalisse was a "simple peasant girl". Ulysses gave up his immortality to be with her.
 * The Doctor's first regeneration took place on Earth when he was a boy, in "tragic" circumstances. Following it, he was taken to Gallifrey to a new life, unaware that he had spent his short first life on the Blue Planet.
 * Aura Force Fields allow the Doctor and Barusa's spirit to venture out on Skaro without being destroyed by the high levels of radiation.

Story notes

 * Doctor Who: Regeneration reproduced multiple "deleted scenes" present in earlier drafts of the Chronicles than the "definitive" version that was printed in the Leekley Bible, and reproduced in full in Doctor Who: Regeneration itself.
 * The early scene of the Doctor bickering with Barusa around the Battle of Waterloo was expanded. The Doctor reminded Barusa that he himself had encouraged the Doctor to meddle in Ancient Greece to give the builders of Athens architectural advice. Additionally, Barusa's angry summary of the adventures he'd partaken in with the Doctor so far had included not only encounters with the Cybs and the Daleks, but also "running after the most immoral woman in the Galaxy, that Time Lord wench, the Rani".
 * The incident at the Cairo Museum was slightly longer, with the joke the Doctor makes about the mummies being reproduced rather than merely mentioned.
 * More adventures are included in the "Adventures in Distant World" section where Barusa inserts brief summaries of adventures (meant to serve as seeds for potential episodes of the rebooted TV series) into his chronicles. These include The Cybs, The Sea Devils, The Outcasts, The Land of Fear, The Pirates, The Claws of Axos, The Daemons, and Shada. Among other changes relative to the original Doctor Who episodes these narratives loosely adapt, Shada would have seen the Leekley-verse's Romana as simply a Time Lord whom the Doctor was taking for a ride to allow her to visit her uncle living undercover on Earth, rather than a long-term companion. The latter "uncle" character would presumably correspond to the classic continuity's Professor Chronotis, although he is not referred to by name.

Continuity

 * Barusa becomes the Doctor's spirit guide. (PROSE: Unnatural History)
 * Before TARDISes were perfected, some of the early Time Lord explorers were lost in time. (PROSE: The Infinity Doctors, Dead Time)
 * Barusa mentions that one of his previous incarnations was a megalomaniac. (TV: The Five Doctors)
 * The Doctor has been a master of martial arts. (TV: Inferno, et al.)
 * The Doctor has a Time Lord father and a human mother, (TV: Doctor Who) Ulysses and Annalisse. (PROSE: The Infinity Doctors)
 * Ulysses was a great Time Lord explorer. (PROSE: Cold Fusion, The Infinity Doctors)
 * The Doctor finds the Lost Scrolls of Rassilon inside a secret mountainous cave. (PROSE: The Infinity Doctors)
 * The Scrolls predict that the Doctor will save Gallifrey from Darkness. (PROSE: Unnatural History, The Gallifrey Chronicles)
 * The Spider Daleks are designed by Davros during the creation of the Daleks. (PROSE: War of the Daleks, Father of the Daleks)
 * Daleks from this universe entered the Eighth Doctor's universe in COMIC: Fire and Brimstone.
 * Spider Daleks are also shown as arising from an alternate creation of the Daleks in PROSE: Engines of War.
 * The Doctor's TARDIS has an Infiniti Chamber through which the cosmos can be viewed. (PROSE: Just War, The Infinity Doctors)