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. (PROSE: The Infinity Doctors)

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

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. (PROSE: The Infinity Doctors)

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)

According to Irving Braxiatel, his father had a cellar full of Draconian brandy. (AUDIO: Everybody Loves Irving) Braxiatel was the Doctor's brother. (PROSE: Tears of the Oracle)

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. (PROSE: Unnatural History)

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 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 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. 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)

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 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

 * The idea of the Doctor's father being named Ulysses originated in Philip Segal's proposed late 1990s revival of Doctor Who and was echoed in John Leekley's Leekley Bible. This was later incorporated into several BBC Eighth Doctor Adventures novels, most notably Lance Parkin's The Gallifrey Chronicles, where Ulysses first appeared under that name. His appearance in those books was based on Sean Connery.
 * In another proposed Eighth Doctor movie script, Robert deLaurentis' 1994 The Time of My Life, the Doctor's father taught at Berkeley College as "John Smith" before being fired for building an atomic bomb as part of an anti-nuclear protest. These events were mentioned as part of Daniel Joyce's backstory in Unnatural History; like Joyce, Smith was married to a woman named Ann with whom he had a daughter. DeLaurentis was thanked in the acknowledgements of Unnatural History.
 * 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.
 * 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. The Doctor's father would also have appeared as a professor from Berkeley in Lance Parkin's unproduced Eighth Doctor novel Enemy of the Daleks.
 * 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.