Ulysses

The Doctor's father, who took on the name Ulysses and also lived under the pseudonym Daniel Joyce, was a Time Lord explorer and renegade.

Life on Gallifrey
In his time at the Academy, the Doctor's father, like his own father, was tutored by Patience, an old friend of the House of Lungbarrow.

Like many other Time Lords of his generation, he had ambitions to change the universe. (PROSE: The Infinity Doctors) He often talked with his friends about wars, great projects, and other big things that had to be taken care of. (PROSE: Unnatural History) He had a seat on the Supreme Council. (PROSE: Cold Fusion)

He often consorted with aliens. For instance, he was close friends with Mr Saldaamir. (PROSE: Unnatural History) He had a cellar full of Draconian brandy. (AUDIO: Everybody Loves Irving; PROSE: Old Ruins) He chose the name "Ulysses" for himself based on the Earth adventurer, becoming one of the first Time Lords to rename himself. On Earth he married Penelope Gate, a human from 19th century England.

When Ulysses, Penelope, and Saldaamir were studying the temporal cicatrix in the Shoal, the three met Lady Larna, a Time Lord from their future. She told them about a Matrix prophecy of the coming War and the Time Lord destined to save Gallifrey.

Unbeknownst to the High Council, Penelope gave birth to a hybrid son. When fellow Time Lord Marnal threatened to expose Ulysses and Penelope, they used the telepathic circuits of his TARDIS to wipe his memory and dumped him in England in 1883 with Penelope's mother. (PROSE: The Gallifrey Chronicles)

When the Doctor was "barely a loomling", he let a cobblemouse loose in the great hall of the House of Lungbarrow while his father was meeting with Saldaamir. The mouse scattered their plans and notes in the air, making the Doctor's father very angry. (PROSE: Unnatural History)

When the Doctor was young, his parents went with him on a trek in the mountains. They owned a summer house on the other side of Kasterborous. (PROSE: The Infinity Doctors) The Eighth Doctor recalled childhood memories of his father holding him up to see the stars (PROSE: The Eight Doctors) and the two lying in the grass watching a meteor storm. (TV: Doctor Who) The Seventh Doctor remembered a time when his father had his arm across the Doctor's shoulders as together they watched a Gallifreyan dawn. (PROSE: Matrix)

The Doctor's father was friends with Savar. Some time before the Doctor finished studying at the Academy, his father stood by his side as he played a chess match against Savar. Later, when Savar left on a mission to find Omega and bring him back to rule Gallifrey, the Doctor's father approved of the plan at first but ultimately chose to stay behind and watch as Savar entered the black hole. (PROSE: The Infinity Doctors)

Neither of the Doctor's parents told him about sex. (PROSE: The Twin Dilemma) The Doctor's father was still on Gallifrey when the Doctor had children.

As a child, the Doctor attended a festival with the entire household and their friends, including Saldaamir, two aliens from Althrace, and a yellow-skinned man with red fins on his head. When the Doctor and Patience danced, beginning to fall in love, the Doctor worried to himself about what his father would think. (PROSE: The Infinity Doctors)

Irving Braxiatel, the Doctor's brother, (PROSE: Tears of the Oracle, The Shape of the Hole) noted that his father had a cellar full of Draconian brandy. (AUDIO: Everybody Loves Irving)

Leaving Gallifrey
He noted to Sam Jones that he had never understood Time Lord teachings about the sanctity of the Web of Time, instead preferring to be unbound by history or the big picture. This resulted in situations like his visit to Youkali, following which the Doctor spent a week "cleaning up" after him. But this perspective led him into trouble, as indicated by the tattoo on his forearm. As a result, he gave up the rank of Time Lord.

A version of history existed where the Time Lords banned all mention of the Doctor's father's name for consorting with aliens. In another version, the Doctor's father deleted every record of himself from the files. (PROSE: Unnatural History) The Infinity Doctor later thought to himself that his father's name was not Ulysses and that he was a professor at Berkeley University on Earth in the 21st century. (PROSE: The Infinity Doctors)

In Berkeley
Sometime in the 1980s, he worked as a professor at the University of California in Berkeley. However, he was fired for building a small atomic bomb as a demonstration that any lunatic could build one. Twenty years later, he returned to Berkeley as "Daniel Joyce", a physics professor purportedly from Cornell University in Ithaca, New York. The Eighth Doctor commented to Joyce that his pseudonym "fit him"; (PROSE: Unnatural History) the novel Ulysses had been written by James Joyce, (COMIC: The Final Chapter) and the mythological Ulysses was the King of Ithaca. (TV: The Myth Makers)

After the millennium Joyce gave Professor Wagg a new beryllium chip to make up for the one that was stolen (PROSE: Unnatural History) from his atomic clock by the Eighth Doctor. (TV: Doctor Who) At this time, Joyce was married to Anne, and they had a daughter in her thirties; however, he also kept a picture of an elaborately gowned, slightly plump redhead in his office. Joyce was very involved in anti-nuclear activism, including writing papers for the Indian-Pakistani antinuclear initiative conference.

In 2002, the Eighth Doctor sought Joyce's assistance in defeating Griffin and closing the temporal cicatrix in San Francisco. Joyce was actually hiring Griffin's Society on the Needle to collect biodata for the Advanced Research Project. Joyce told the Doctor that he had begun experimenting with his biodata at this time, but refused to tell him why. At the time, he was being assisted by Larna. (PROSE: Unnatural History)

Later fate
Although, early in his travels with Rose Tyler, the Ninth Doctor had expressed a certainty that he was the only Time Lord left in existence, (TV: Dalek) and the Tenth Doctor also thought himself to be the last of his kind, save for the Master, (TV: Last of the Time Lords) when Quintus asked the Tenth Doctor not to tell his father, Lobus Caecilius, that he had showed the Doctor Lucius Petrus Dextrus's house, the Doctor responded, "Only if you don't tell mine." (TV: The Fires of Pompeii)

However, the Thirteenth Doctor later stated that "her entire family" had died a long time before the Twelfth Doctor's regeneration. (TV: The Woman Who Fell to Earth)

Legacy
The First Doctor had a dream of his father sending him out into a body of water in a leaky boat. The image of his father was distorted in the dream, resembling that of a stuffed bear. When the Doctor woke he found himself in the TARDIS holding HiFi. (PROSE: The Three Paths)

The Eighth Doctor could remember both being Loomed and having a father. He knew one of these was a dream, but he was unsure as to which. (PROSE: The Shadows of Avalon) Maris' potential engine gave several different origins for the Doctor. In one of them he had a Time Lord father and a human mother. (PROSE: Celestial Intervention - A Gallifreyan Noir)

As an amnesiac in the post-War universe, (PROSE: The Burning) the Eighth Doctor remembered that he was immortal on his father's side. The sentient quantum field of the planet Albert later told the Doctor that there was a reality where he knew his father's face. (PROSE: Grimm Reality)

Ultimately, the Doctor chose to think of the universe as his foster family after his parents "decided to opt out of their responsibilities." (PROSE: Beltempest)

once referred to Wilfred Mott as the Tenth Doctor's "dad". Wilfred responded by saying that he would be proud if he was. Later, the Doctor reciprocated the compliment. (TV: The End of Time)

Helios, a man at the very end of the universe who was thought to have been Merlin and who had memories of a family like the Infinity Doctor's, claimed that he'd came to the Needle to continue his father's work. Through this work, Helios was highly concerned with preventing Last Contact. (PROSE: The Infinity Doctors)

Identity as a Doctor
By some accounts, every generation on Gallifrey since the Intuitive Revelation followed a similar pattern, in large part due to the stasis perpetuated by looms. As seen with Hedin, even names and titles were passed down by lineage, such that descendants played identical roles as their forebears. (PROSE: The Infinity Doctors) The Doctor was only the most recent of a long patrilineal line of Time Lords who had held similar positions in Time Lord society, being great explorers, progressive members of the Supreme Council, and companions to Patience. (PROSE: Cold Fusion, The Infinity Doctors) When faced with contradictory memories, such as having multiple accounts of leaving Gallifrey, having been the Doctors seen in the mind battle with Morbius, and having lived for thousands of years and through about 130 incarnations, the Fifth Doctor had a vision of the First Doctor leaving Gallifrey. Commenting on this vision, the other described it as both how the Doctor's life began and how it ended, saying, "Time is relative. History repeats itself, and repeats itself again. Father to son." (PROSE: Cold Fusion)

Several details indicate an overlap between Ulysses and early Doctors: one of the Doctors seen in the battle with Morbius was said to have famously embarked on an Odyssey (PROSE: Cold Fusion) and the Infinity Doctor, who possessed a possible overlap with those Doctors, had a deep love of the Iliad. The Infinity Doctor was even certain that his father was not named Ulysses. (PROSE: The Infinity Doctors) Both these Doctors remembered being charged with "consorting with aliens" during the loom-born revolt; (PROSE: Cold Fusion, The Infinity Doctors) a Faction Paradox boy noted that in one version of history Ulysses had been punished for "consorting with aliens". Ulysses' collaboration with Larna also echoed the Infinity Doctor's friendship with her. (PROSE: Unnatural History)

Appearance
Ulysses was powerfully-built (PROSE: The Infinity Doctors, The Gallifrey Chronicles) with white hair and a short beard. (PROSE: Unnatural History, The Gallifrey Chronicles) In the portrait hanging over the fireplace in the Infinity Doctor's chambers on Gallifrey, he had rugged features, a weathered face, and dark eyes. (PROSE: The Infinity Doctors) On Earth, "Daniel Joyce" had a tattoo on his forearm that he had tried to remove. He had a creases around his eyes and a Scottish accent. (PROSE: Unnatural History)

Behind the scenes

 * Kate Orman, co-author of Unnatural History, said it was "absolutely clear" in her mind that Daniel Joyce "seduced and carried away" the 18th century human Penelope Gate (from Orman's earlier novel The Room With No Doors), then abandoned her to raise their son on Earth. This was meant to explain the Fifth Doctor's statement in Black Orchid that, as a boy, he had always wanted to drive a steam train.
 * Marc Platt stated that in Lungbarrow, he intended Leela and Andred's first child to be the Doctor (or, rather, the Other, who would one day be reincarnated as the Doctor), making Andred, in one sense, the Doctor's father. However, while this was hinted at in the novel, it was never explicitly confirmed.
 * Philip Purser-Hallard theorised on Twitter that the Woman played by Claire Bloom in The End of Time, who was conceived by Russell T Davies as being the Doctor's mother, could actually be the Doctor's father owing to Time Lords being able to change genders on regeneration.

Origins
The concept of the Doctor's father originated in various script proposals for Philip Segal's planned 1990s revival of Doctor Who. In these proposals, the Doctor's father was the son of Borusa and heir to the Sash of Rassilon.
 * In John Leekley's Fathers and Brothers, Ulysses was "the Great Explorer", a hero of Gallifrey. After having a son on Gallifrey, the Master, Ulysses fell in love with a human woman and had another son in ancient Egypt. There Ulysses taught the Egyptians to build the pyramids and reigned under the name Cheops. However, when his son fell ill with River Fever, Ulysses sent him back to Gallifrey for medical attention; then, when his wife died of the same fever, he tried to return himself. However, his TARDIS had been stolen by the Master, who wanted a clearer line of succession, and Ulysses was stranded on Earth. Borusa kept the child's half-human nature secret so he could attend the Time Lord Academy, and he became known as the Doctor.
 * A somewhat different version of this story was recorded in The Chronicles of Doctor Who?, the narrative spine of the "Leekley Bible". The story would go on to be made public in Doctor Who: Regeneration, and it was established as a valid parallel universe to the Eighth Doctor's life in Fire and Brimstone.
 * The Doctor's father's name was given as Ulysses in The Gallifrey Chronicles, and his post-regeneration description as "powerfully built, rugged features, weathered face with dark eyes" matches the description given of the Doctor's father in that novel and The Infinity Doctors, where his appearance was based on Sean Connery.
 * In Robert deLaurentis' The Time of My Life, the Doctor's father was "Dr. John Smith", an explorer who fell in love with a human woman in the early 20th century. She died after giving birth to a son and, knowing that he could not care for the baby alone, Smith sent him to Borusa on Gallifrey. Shortly afterwards, Smith joined Operation Black Cross, an OSS team which tried to assassinate Hitler; after the Master informed the Germans about the plan, the team was captured and Smith was imprisoned in . Following the end of the war, Smith moved to America, where he published scientific papers at Princeton, Chicago, Brown, Duke, and finally UC Berkeley, where in the 1970s he was fired and nicknamed "Doctor Doom" after building a small atomic bomb as part of his anti-nuclear activism. He started writing science fiction novels about "The Traveller" and married his research assistant, Professor Anne Baker of the Berkeley Physics Department, who he called "Q-Star"; they had a daughter and grandchildren.
 * These events were referenced as part of Daniel Joyce's backstory in Unnatural History, where he has an obscured concentration camp tattoo, he was fired from Berkeley for building a bomb during an anti-nuclear demonstration, and he is married to Anne and has a daughter. DeLaurentis was thanked in the acknowledgements of Unnatural History.

Other appearances

 * Lance Parkin's unproduced Eighth Doctor novel Enemy of the Daleks would have further explored the Doctor's father. In that pitch the Doctor would have discovered that his father, while masquerading as a professor at Berkeley, was leading an intergalactic coalition dedicated to fighting the Enemy and stopping "Last Contact" from occurring and making the War in Heaven inevitable. The story would have introduced the Klade as a part of this coalition; in Parkin's later book Father Time the Klade were shown to live on the Needle, just like Joyce's "Society" allies in Unnatural History.
 * Jon Blum, co-author of Unnatural History, intended to feature Joyce under another pseudonym in a planned Eighth Doctor novel entitled The Why Knot. The pitch was ultimately turned down by range editor Justin Richards.
 * Joyce and his wife Anna appeared in Jonathan Dennis' The Killing of a Flash Boy, published in the 2001 charity anthology Missing Pieces. In the short story, the Eighth Doctor entrusted the couple with raising a boy with psychic powers being hunted by UNIT. Larna was also mentioned.