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Ulysses was a renegade Time Lord explorer. He was the Doctor's father.

Biography
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 big things that had to be taken care of. (PROSE: Unnatural History)

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 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 on Earth in England, 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 on a trek in the mountains with him. 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 to watch 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 his 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)

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 and his father's names 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 was a professor at Berkeley University on Earth in the 21st century, but his name was not Ulysses. (PROSE: The Infinity Doctors)

Sometime in the 1980s, he worked as a professor at the University of California in Berkeley, working on the Advanced Research Project. 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)

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. He often referred to the Doctor as "son".

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 his 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)

Appearance
Ulysses was powerfully built with white hair and a clipped beard. (PROSE: The Gallifrey Chronicles) On Earth, "Daniel Joyce" had a tattoo on his forearm that he had tried to remove. He had a short white beard and a Scottish accent. (PROSE: Unnatural History)

Behind the scenes

 * The Doctor's father being named Ulysses originates in the Leekley Bible, John Leekley's proposal for a late 1990s television revival of Doctor Who. 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.
 * 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 after Daniel Joyce "seduced and carried away" Penelope Gate, he 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 also have explored the "professor at Berkeley" incarnation of the Doctor's father. In that pitch, the Doctor would have discovered that his father was the leader of an intergalactic coalition dedicated to fighting the Enemy and preventing the War in Heaven. The story would have introduced the Klade as part of this coalition; in Parkin's later novel 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 yet another pseudonym, in a planned Eighth Doctor novel entitled The Why Knot. However, it 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.