When the Doctor’s father was incarcerated in Shada for “consorting with aliens,” the name Ulysses erased from Time Lord records, he merely had to bide his time. There would be no grand escape attempts, no rebellions. He didn’t need to wait for the Carnival Queen to burrow into President Romana’s skull and twist, setting free the Grandfather and the hordes of Shada’s criminals.
His son’s origins and timelines changed with every regeneration, every biodata twitch and genetic temporal kick. At one point, the Doctor became a Time Lord without a father, without parents, a God reincarnated and sewn on a singing wooden loom laced with twitching and fleshy threads.
With a sigh, a man made temporal impossibility simply shuffled out of his cryo-chamber or dreamscape. The prison at the heart of History itself, watching it as a secondary Eye of metal and rock, did not see a non-existent concept, and he merely walked out of Shada.
Later, Professor Daniel Joyce entertains a guest, allowing himself to be open and curt regarding his relationship with the Doctor and his tangled history.
“His... shall we say his narrative, it tends to shift and change. Not just present and future, but his past. It becomes something as fluid and conceptual as Gallifrey’s, really. Legends and myths, all conflicting and contrasting and impossible. I managed to slip through one of these narrative blips. A break in my need to be there for him.”
“You act, of course, like you’re the original. The real thing. The true history, always there when his biodata... erm...”
“Acts out?” He smiled at her. “Of course. Fathers are always there at the end of a bout of teenage rebellion.”
“... but have you ever considered that all of that, your history, your... perception of his, is just one of those narrative blips?”
“Like, this Doctor. My Doctor. Velvet and curls and sandalwood.” She bit her lip, wondering if she’d gone too far. Might as well see it through. “What if you... only exist and have always existed just because of his narrative shift?”
“Of course I’ve considered it.” His voice was soft, kind, and his smile was still warm as a tea mug. “It would be interesting, wouldn’t it?”
“But I have too much to work on and focus to dwell on existential theoreticals. I prefer to think, either way, that I’m just here when he needs me.”
“I always assumed there was some tension.”
"Of course. As in any family."
“... doesn’t he, like... have to clean up temporal messes and chaotic experiments you leave behind on occasion?”
“Technically that’s needing me.”