#cold fusion

Okay, ground rules first. Anything seen on tv, happened. I can recontextualize as much as I want (and I'm gonna do that, believe me) but it still has to fit with everything we see onscreen. I also have to use all of an EU source if I use it. No picking and choosing bits. However, that same loophole applies to EU material - I can recontextualize those as much as I want, too.

With that out of the way, let's meet the stories that are our players. I'm going to be sorting them into medium by category this time.

Tv stories:

Ascension of the Cybermen / The Timeless Children: The controversial Thirteenth Doctor episodes. I'm assuming you're familiar with if you're reading this.

Fugitive of the Judoon: The Thirteenth Doctor story that introduced the Fugitive Doctor. I'm assuming you're familiar with this.

Flux: The Thirteenth Doctor story that followed up to the Timeless Child plot points in a way that is very relevant to this discussion. I'm assuming you're familiar with this.

A Good Man Goes to War: An Eleventh Doctor episode that established some of the history of the Time Lords

The Brain of Morbius: A Fourth Doctor story. Notable for this discussion because it featured brief images of ten faces that were implied to be incarnations of the Doctor from before the First Doctor. These are collectively known as the "Morbius Doctors".

State of Decay: The Fourth Doctor tv story that established the series lore on vampires

Books:

Cat's Cradle: Time's Crucible: the Seventh Doctor book that laid the groundwork for Lungbarrow and its Gallifrey Lore

The Pit: A 90s Who book with some vampire lore

Goth Opera: A 90s Who book with some vampire lore

Damaged Goods: A 90s Who book with some vampire lore

Cold Fusion: A book starring the Fifth and Seventh Doctors that is notable for introducing the character of Patience

Lungbarrow: the big Gallifrey Lore book. I will be going over this one in depth

Interference: Shock Tactic: A 90s Who book with some vampire lore

The Infinity Doctors: A very confusing Doctor Who book (this will get explained later)

The Book of the War: The first book in the Faction Paradox series

Audios:

Zagreus: A Big Finish story starring the Eighth Doctor and Rassilon

Patience: A Big Finish story starring the Eighth Doctor

Comics:

The Tides of Time: A 70s comic starring the Fifth Doctor

The Bidding War: A 2010s comic with some vampire lore

Monstrous Beauty: A 2020s comic with some vampire lore

Origins: A recent comic that features the Fugitive Doctor

Okay, so there are kinda four threads running together that tell a more complete story, but were all written independently of each other. The story of the Timeless Child and Division, the story of the Other, the story of Patience, and the story of the Yssgaroth War. Let's go through them in order.

Also while the Other, the Timeless Child, Patience's husband, the Fugitive Doctor, the Infinity Doctor, the Morbius Doctors, and the Doctor are all presented as more or less the same character who all call themselves "the Doctor", I will be referring to them all separately. I have a few reasons for doing this which will become clear later, but it's also helpful for reasons of clarity.

Prologue: Where all this mess came from

So in the 70s, there was a tv story called The Brain of Morbius. Morbius was a Time Lord president who decided it was Morbin Time, tried to conquer the universe, and caused a civil war on Gallifrey in just about the only interesting thing to happen on Gallifrey between Rassilon's presidency and the Doctor being loomed. He was killed, but one of his followers managed to save his brain and is trying to make Morbius a new body so it can be Morbin Time again. The Time Lords decide to throw the Doctor at this problem, and he ends up getting into a mind-bending contest with Morbius (who was by that point in an artificial body). During this, both Morbius and the Doctor's past incarnations are shown on a screen, and then we see ten new faces while Morbius says, "How far, Doctor? How long have you lived?". A lot of people assumed those faces were Morbius's, but the intention from the producers was that they were prior faces of the Doctors (I will be referring to these incarnations as the Morbius Doctors moving forward, as that is how they are generally reffered to in the fandom). Trouble is, the rest of classic who completely ignored that.

Oh and if you're worried, while Morbius won the mindbending contest, it left him disoriented enough that he was able to get mobbed by the Sisterhood of Karn and pitched off a cliff, averting the renewal of Morbin Time.

And with that out of the way, let's get on to the real attractions.

Part 1: The Timeless Child and Division

So this story is the most straightforward of the three. In Ascension of the Cybermen / The Timeless Children, it is revealed that in Gallifrey's prehistory, a Gallifreyan scientist named Tecteun travelled off-world (in her world's first exploration of another planet) and found the Timeless Child by a portal to another universe. She took the Timeless Child back to Gallifrey and discovered that the Timeless Child had the ability to regenerate. Tecteun was able to synthesize this regenerative power and give it to her own people, becoming one of the founders of modern Time Lord society in the process. Later on, the Timeless Child and Tecteun were both recruited into something called Division, a time-active-interventionist group that skirted around or outright ignored Gallifrey's laws. It is also stated that the Timeless Child's memory was wiped - at least once, possibly more than once - in order to control them. It's also suggested that Tecteun seems to have regrets about all of this, given how she left a message for the Timeless Child in the matrix about it.

This is where the story gets fuzzy. The next time we see anything, the Timeless Child has evolved into the Fugitive Doctor. She is seen working for Division in the flashbacks in Flux and Origins, but following Origins, she goes on the run from them. The events of the Fugitive Doctor's flight from Division play out in Fugitive of the Judoon. She is able to assassinate Gat, the Time Lord seeking her capture, and while it comes at significant personal loss, there is nothing to indicate that the Fugitive Doctor is unable to make a clean getaway.

By the story presented in Ascension of the Cybermen / The Timeless Children, however, the Fugitive Doctor is assumed to have been captured with her memory wiped to eventually become the Doctor. Let's put a pin in that assumption, though. That same story also shows the Fugitive Doctor and the Morbius Doctors being a part of the Doctor's past.

Tecteun, meanwhile, had become head of Division (if she wasn't head of it to begin with). Origins briefly shows her leading Division at the time of the Fugitive Doctor, and she is finally shown meeting the Doctor proper in Flux. There, it is revealed that she had started considering the entire universe a scientific experiment, but due to the Doctor being considered too much of a rouge element, she decided to use antimatter called flux from outside the universe to destroy the universe, with Division being safe outside the Universe. She also released a pair of Great Old Ones, Swarm and Azure, with the intention that they would kill the Doctor. Tecteun's plan was that the old universe would be destroyed, and that Division would conquer the universe that the Timeless Child originated from.

This plan did not work.

Swarm and Azure instead killed Tecteun and destroyed Division, before being destroyed by an entity only known as Time (and I could go on a whole tangent on what her deal is, but I'm gonna save that for another post). It's not shown explicitly in the show, but I also believe Time removed the destruction of the flux from the universe as well (mostly because planets explicitly destroyed in Flux are shown still existing in the future of the series).

In any case, during the Flux event, the Doctor was able to recover the archive where the Timeless Child's wiped memories were stored, but she ultimately decided not to access them.

It's never stated which universe the Timeless Child comes from in the show, but we're gonna circle back to that. It's also not stated how long Tecteun ran Division between its founding in early Gallifreyan history and its destruction during the Flux event. We're coming back to this, too.

Part 2: The Other

Cat's Cradle: Time's Crucible establishes two very important things about Gallifreyan history. One, all Time Lords became sterile early in their history - shortly after the conclusion of their war with the vampires (more on that war in a bit). Since then, instead of having sex, they have big cloning machines called Looms that make new Time Lords. And two, Rassilon (the founder of Time Lord society) had two major co-founders - Omega, and one other whose name was lost to time. He gets called just "the Other."

Rassilon and Omega were both established as characters in the classic series, but the Other is an invention of the books in the 90s (from the reader's perspective at least - he was a behind the scenes idea from the last few seasons of classic who, but he was never explicitly mentioned onscreen). He gets cryptic references all over the Virgin New Adventures book line, but this only gets concrete in their final Seventh Doctor book, Lungbarrow.

Where we get to know them in the book, Omega is presumed dead, and the Other and Rassilon are having a falling out. Omega's death is weighing heavily on the Other, and he thinks Rassilon is going power-mad and is trying to have the Other killed. Omega's last and most impressive creation, the stellar manipulator called the Hand of Omega, is quite possibly the Other's only friend by this point. The Other wants to leave the planet and so he tells his family to escape, and then confronts Rassilon with his intentions. Rassilon Does Not Like This and tries to have the Other stopped, and blocks all spaceports to make this happen. The Other then calmly walks into the primary generator for the looms and is never seen again.

And then, ten million years later, out from a loom, comes the Doctor. The Doctor's looming process was unusual, with the Doctor later claiming he could remember just before it happened, waiting to be born. (Although given the Doctor was five years old at the time he said this, that may be a little suspect). In any case, the Doctor lives a fairly normal life for a while, until he is found by the Hand of Omega which sees in him its old master. Shortly thereafter, the Doctor is confronted by the Time Lord Glospin (explaining his deal is a little complicated but he's a part of the same Family House as the Doctor is, the titular House Lungbarrow), about some irregularities in the Doctor's biology before being driven off by the Hand. It's ambiguous if either of these were the deciding factor, but the Doctor takes the Hand and leaves Gallifrey shortly thereafter.

Of course there's one last little piece left to take care of. If you're familiar with Classic Who, you may know that when we first met the Doctor, he was travelling with his granddaughter, Susan.

Lungbarrow claims that the Doctor's first trip in the Tardis was to travel back to Gallifrey's prehistory and meet the Other's granddaughter, the last child born before the Time Lords became sterile. She recognizes the Other in the Doctor, and considers him her grandfather. The Doctor doesn't quite recognize her, but takes her on as his first companion in the Tardis. And thus, Susan joined the Tardis crew.

The other thing that's important is uh that Lungbarrow has an actual plot. And said plot is only tangentially related to the above. Everything I just said is presented as three flashbacks in Lungbarrow - one straight narrative sequence (the argument between Rassilon and the Other), one where the Doctor shares his memories of leaving Gallifrey (basically everything that happens with Glospin, the Hand of Omega, and the Doctor first leaving Gallifrey), and one where several characters enter the Doctor's subconscious and have a dream sequence (including the Other walking into the Looms and the Doctor meeting Susan). The subconscious trip has some moments to it that are super trippy and metaphorical, and I'm gonna use that fact later. But for now, on to part 3!

Part 3: Patience

Like I said earlier, Cat's Cradle: Time's Crucible is the story that establishes that all Time Lords are sterile. At the end of a civil war in Gallifrey's ancient history, the leader of the losing side, Pythia, cursed the people who would become Time Lords with sterility before killing herself. (Her followers, by the way, left Gallifrey and eventually became the Sisterhood of Karn). The Time Lords, desiring to avoid extinction, created breeding engines known as Looms, which would create new Time Lords through what was effetely cloning. That's the story presented in Cat's Crade: Time's Crucible, anyway. But if you look at other places in the EU, this story starts to crack. An Earthly Child introduces Susan Forman's explicitly biological son, for example. And in Lungbarrow, the Time Lord Andred is able to get a human, Leela, pregnant, although the character's future appearances in Big Finish are notably child-less, suggesting the pregnancy failed somehow (either that or the child removed themselves from history as part of joining faction paradox and became the character known as Intrepid, but this is a tangent).

So are Time Lords sterile? Yeah, I think so. For the most part. But we know that not all of them are. A rare few can still reproduce sexually. There is another Time Lord who had a biological child that I've yet to bring up, as well. Her true name was lost to time, so we know her only as Patience.

This is her story.

The character of Patience has some truly strange origins, even for the Doctor Who EU. In the 1982 comic The Tides of Time, the fifth Doctor briefly sees an illusion of someone who looks familiar to him, created by the demon Melanicus using something called the Event Sythesizer (no, I'm not going to explain that). The art shown is close enough to Second Doctor companion Zoe Herriot to assume that's who the author and artist intended the illusion to be of, but that's not the direction later stories went in.

The character of Patience was introduced proper in 1996's book Cold Fusion. It also features the Fifth Doctor, in an earlier point in his life then The Tides of Time. In it, a prototype Tardis crashes into a planet that is later colonized by humans. The humans discover one pilot, comatose, who by all rights should be dead. She isn't. They take her back to their big fancy lab and attempt to find out more about her with basically no success.

Enter the Doctor. (And also Tegan Jovanka.)

When the Fifth Doctor stumbles into this, he is able to help the pilot complete her first regeneration. She is unable to remember much of anything from prior to her regeneration and is from Gallifrey's distant past. She is, biologically, something of a proto-Time Lord: she speaks a different language then the Doctor naturally, she only has one heart, and a few other things. She's explicitly more-or-less a contemporary of Rassilon.

Not having a name for herself, she adopts the moniker "Patience" on Tegan's unintentional suggestion. Despite all this, Patience and the Doctor recognize each other on some level, and neither really have any ideas as to why - the Doctor shouldn't even be able to recognize the dialect of Gallifreyan she speaks, as it is dead by his time. Patience has some garbled memory of fleeing from arrest as ordered by Rassilon (with the implication being that any fertile Time Lords were having their births stopped so that the loom-born were to inherit Gallifrey). Patience's escape came with the help of her husband, whom authorial intent confirms as one of the Morbius Doctors. In any case, in the present day, Patience is starting to properly recover when she is shot in the back of the head, apparently killing her. Her body then disappears. The Fifth Doctor's memory of Patience is lost shortly thereafter when the Seventh Doctor orchestrates the Fifth Doctor losing his memory of the whole adventure in order to preserve the timelines. The Seventh Doctor only met his prior self after Patience's body had vanished, meaning that the Doctor's entire memory of Patience was erased - except, perhaps, for some vague recollection which we see in The Tides of Time.

While Patience's fate is followed up in the book The Infinity Doctors, The Infinity Doctors is a very strange book that doesn't really contribute much to this ongoing discussion. The Infinity Doctors is deliberately evasive about which Doctor it stars, with its protagonist being sometimes implied to be the First Doctor and sometimes the Eighth. It's very possible that Patience and Omega (yes he's here but I'm not going to explain that) are the only characters in the story from the Whoniverse as we understand it, with everyone else being from a different universe. I might do a breakdown of The Infinity Doctors someday, but now is not that day.

The only other information we have about Patience comes from the 2021 audio story fittingly entitled "Patience". In it, the Doctor tells uses an ancient artifact that takes the form of a deck of cards called the Paradoxica to analyze time and hide his companions - Liv Chenka, Helen Sinclair, Tania Bell, and Andy Davidson (yes, the Torchwood character. no, I'm not explaining that either) - from the Judoon. The narrative is interspersed with the Doctor telling a fairy tale about a woman completing an impossible task (emptying an ocean with a bag that had a hole in it) and receiving the child she desired once she had spent an eternity completing this task. The story ends with the confirmation that this woman was Patience, and that she gave the Doctor the Paradoxica. How this happened is left unsaid - either she gave it to her husband who became the Doctor, or this happened during the events of Cold Fusion.

Part 4: The Yssgaroth War

Unlike the other narratives I've just rambled off, the Yssgaroth War is much more of a patchwork from various places around the EU, so this is gonna be even more scattered than I have been thusfar.

State of Decay, for being a story set in the pocket universe called E-Space, ended up being one of those foundational Gallifrey lore episodes of the classic series. That's the serial that established that at the dawn of time, the Time Lords fought and won a massive war against the vampires.

Yes, you read that right. This is one of my favorite pieces of Doctor Who lore.

State of Decay establishes that the Great Vampires were massive bat-like creatures who could drain the life from entire planets and who created more traditional vampires as their servants. Rassilon lead Gallifrey against them, and ordered the construction of "bowships," which were giant spaceship crossbows that could be used to stake the Great Vampires. The Great Vampires were ultimately defeated by the Time Lords. EU sources generally agree that this was the biggest war the Time Lords ever participated in until the Time War ten million years later.

The book The Pit would add a couple of new details about the conflict. It would rename the Great Vampires "Yssgaroth" and claim that the Yssgaroth originated from outside the universe - the early time travel experiments overseen by Rassilon ripped a hole in reality and the Yssgaroth were what came through with intent to consume the universe. These details are supported by Cat's Cradle: Time's Crucible and Interference: Shock Tactic.

A couple more recent comics have fleshed out the Yssgaroth War a bit. The Bidding War further reinforces that the Yssgaroth are from outside our universe, with it showing that during the Time War, the Time Lords opened a rift to the Yssgaroth dimension in an attempt to use them as a weapon against the Daleks. Monstrous Beauty was the first story to show us the War proper, depicting Rassilon personally leading forces against the vampiric army.

And this would all be interesting but irrelevant to our discussion if not for two stories published in the early 2000s that both seek to recontextualize the Yssgaroth War and the Time Lord's rise to power.

Let's start with Zagreus. The story as a whole is dedicated to deconstructing Rassilon's façade as a benevolent and reasonable ruler and instead reveals him to be a xenophobic tyrant who wished to remake the universe in his image - something that lines up with pretty much all of Rassilon's appearances post-Zagreus. As part of this, the vampire Lord Tepesh states that before the war, the vampires were peaceful and Rassilon provoked them because he feared their power. Tepesh is presented by the narrative as an unreliable narrator, but the point he makes is still worth noting.

The other story I need to talk about is The Book of the War. While the book's primary focus is The War in Heaven (for the uninitiated, that's basically spin-off series Faction Paradox's version of the Time War), it does give a lot of relevant information about the Yssgaroth War. First of all, it gives the timing of the War being right after Gallifrey established History as a concept - by "anchoring the thread" and making a linear history, the Time Lords accidentally let the Yssgaroth into the universe. While this contradicts some of the timings given by some of the sources mentioned above (other sources agree that it was the early experiments that caused the Yssgaroth to enter the universe not the final establishing of History and mastery over time), this can be excused since The Book of the War is an in-universe document and so may not be completely accurate. What makes this book relevant is that it also theorizes that the Time Lord's regenerative capabilities were stolen from the vampires. Even for an unreliably narrated book, this is treated as speculation, but as a concept, that is fascinating.

Interlude: when regeneration happened

There is some inconsistency in all of these sources as when regeneration first became a property of the Time Lords. The Timeless Children has it come shortly after they discover interstellar space travel, and far before time travel, but several of the VNA-era books (including Cold Fusion and I think Cat's Cradle: Time's Crucible) depict early time-travelling Gallifreyans as being without regeneration. The tv episode A Good Man Goes to War states that regeneration came about as a result of exposure to the Time Vortex. My personal take is that The Timeless Children showed Tecteun discovering regeneration, and initially only shared it amongst herself and her elite (Rassilon, etc.). After the Looms went into effect, they started Looming more and more Time Lords with regenerative capabilities, until eventually it's a shared trait among all Time Lords. After ten million years, the artificial origins of regeneration have been lost to time, but the symbiotic nature of the Time Lords to Tardises and the Time Vortex has meant that a being conceived in a Tardis could be engineered to have limited regenerative capabilities.

Part 5: Bringing it all together

So back to the Doctor and Gallifreyan history. Uh, how does this all make one cohesive story?

Okay so our story starts with Tecteun and finding the Timeless Child by a portal to another universe. She takes said child home, discovers from it the secrets of regeneration, and so on and so forth. Tecteun, Rassilon, and Omega become the three founders of Time Lord society.

So that's the first thing there. The Other, as revered in Time Lord history, isn't the Doctor or some version thereof. The founder whose name was lost to time was Tecteun. And Tecteun discovered regeneration from the Timeless Child. This child, for whatever reason, starts calling themselves the Doctor.

But wait? Wasn't there some theories running around that the the Time Lords stole regeneration from vampires? And that vampires initially weren't as hostile to the universe before Rassilon saw them as competition?

Yes, yes, there were. It's simple, really. The Timeless Child was from Spiral Yssgaroth. They're a vampire.

(I really wish I had been clever enough to come up with that on my own, but I'm not. Pretty much everything else here is out of my own brain, but that is a fan theory I saw on the internet.)

In any case, the Yssgaroth War was motivated, at least in part, by the Vampires' outrage that their secrets and child had been stolen. But, as history records, they were defeated.

And for a time afterwards, Tecteun and Rassilon continue to rule Gallifrey together. But Omega's apparent death shortly after the end of the Yssgaroth War weighs heavily on them both - and they're both ambitious enough to not quite appreciate the other being their equal. Trouble is, they kinda need each other. Rassilon, despite his posing, isn't a scientist - he's a politician. He needs his scientists to continue to work miracles, and Omega is already gone, so that just leaves Tecteun. Tecteun, for her part, is no leader. She wants power but doesn't have the people skills. And she still cares deeply about her people and about the vampire she has come to see as her child. The two drift apart - Tecteun becoming the leader of Division which she took increasingly off-world while Rassilon becomes more and more the sole face of leadership on Gallifrey.

Eventually this reaches a boiling point. Tecteun and Rassilon have lost all trust in each other. Tecteun makes preparations - including leaving the message in the Matrix we saw in Ascension of the Cybermen / the Timeless Children. She and Rassilon then have the confrontation that we saw in Lungbarrow. But Tecteun doesn't throw herself into the looms - she takes herself off Gallifrey through technology Rassilon doesn't know about and begins to cut Division's ties with Gallifrey altogether. Division has already begun recruiting across the universe, so she figures she can leave Rassilon to his one planet. Notably, she also leaves the Hand of Omega behind on Gallifrey, where it is eventually put in a vault and forgotten about. She maintains contact with Gallifrey only through her agents, one of which is the Timeless Child.

For their part, the Timeless Child has gone through several incarnations. They've had their mind wiped to hide that they're not Gallifreyan, and they have then been the Morbius Doctors, including Patience's husband. The Timeless Child has had a personal life (as seen by their marriage to Patience), but they're increasingly being a full-time agent of Division.

In any case, right now the Timeless Child is the Fugitive Doctor. And she plays along with Tecteun for a while. However, following the events we see in Origins, she goes on the run. Tecteun has Division track her to Earth, where the events of Fugitive of the Judoon play out. The Fugitive Doctor manages to get away as we see, but she doesn't know of any way to get away from Division long-term (as Big Finish is currently exploring) - and, away from Tecteun's influence and protection, she's starting to work out that she's not the Gallifreyan she thinks she is.

In an act of desperation, she pilots her Tardis back to Gallifrey - on the very same day Tecteun left. She takes Tecteun's place in Lungbarrow's story, and throws herself into the Looms, where she dies, dissolving into the giant vat of Gallifreyan genetic material.

This leaves Tecteun searching time and space desperately for the Timeless Child. At first, the Timeless Child seems nowhere to be found. But eventually Tecteun discovers that there is a time traveler called the Doctor out and around the universe. An investigation into the Doctor reveals that they've been all over the universe. Trying to just grab them and do a memory wipe isn't an option because they've done too much. Tecteun doesn't realize this Doctor is a different person to the Timeless Child, to the Doctor they left a message in the Matrix for.

Tecteun had probably never been that good of a person, but she used to care. She used to care about Omega, but he's gone. She used to care about Rassilon, but they burned too many bridges. She used to care about her vampiric child, but she takes this as a betrayal. And whatever good left in Tecteun dies.

Tecteun decides to destroy the universe and start over in a new one where she can control everything, so she picks a point far in the future where Gallifrey will have been destroyed naturally so her home planet will be unaffected. By convivence, one of the Doctor's most common destinations - Earth - happens to be at that point. Tecteun initiates the Flux event in Earth's time and releases Swarm and Azure to finish the Doctor off.

The Doctor stumbles into this, but she's operating off incomplete information from the Matrix. She doesn't realize that she's not the Timeless Child, since the Master seemingly destroyed any records that she could check his claims against. So when Tecteun and the Doctor confront each other, they both assume that the Doctor is the Timeless Child.

And this becomes a moot point because the Doctor finding Tecteun and Division HQ allows Swarm and Azure to find it as well. They kill Tecteun and destroy Division. If you're reading this, you probably watched Flux, you know how this goes.

It's not clear if Rassilon is aware that Tecteun died shortly after their argument. He certainly comes to the conclusion that she won't be an ongoing concern anymore, and, as the last survivor of Gallifrey's founding trio, uses his remaining lives to rule Gallifrey unopposed. With no one to oppose him, he removes Tecteun's name from record - as far as he's concerned, she betrayed him and does not deserve to be remembered.

Ten million years pass.

The House of Lungbarrow looms a new Time Lord, but, for whatever reason, this particular Time Lord has a significant amount of the Timeless Child's genetic material mixed into their genetic soup. This new Time Lord chooses to call themselves the Doctor - in unconscious echo of their genetic predecessor. Their amount of vampiric genetics makes them genetically distinguishable from other Gallifreyans if close examination is done, but for a while no one has any reason to do this.

This is also why I get to call the Doctor a dhampir - they're not a true vampire, but have a nontrivial amount of vampiric genetics - or, to use the terms of The Book of the War, they carry the Yssgaroth Taint.

These genetics are still enough to get the attention of the Hand of Omega, which has been mothballed for those Ten Million years. Maybe the Hand sees the Timeless Child in the Doctor, or maybe it's just intrigued by someone who isn't just another Time Lord. In any case, Glospin confronts the Doctor, the Hand drives Glospin off, and the Doctor leaves Gallifrey with it.

He also leaves with Susan. She isn't from the dawn of Gallifrey. Instead, she is a Loomed Time Lord of the Doctor's era who found herself ostracized and disliked. That being said, she found community with three other Time Lords: the Doctor, the Master, and another Time Lord named Braxiatel. The four of them are all outsiders from their own Houses, and so consider themselves a house unto themselves, and Susan, as the youngest, began referring to the Doctor as "Grandfather", as that term is reserved for the head of a House (something that is established in The Book of the War), as she views him as the head of their little house of four.

In any case, the Doctor and Susan leave Gallifrey. The Master loses his mind when he realize he got left behind, steals a Tardis himself and heads out after the family he thinks abandoned him. Braxiatel stays behind and becomes a successful politician and art collector.

A couple hundred more years pass.

We're now in the events of Lungbarrow. The Doctor shares his memory of leaving Gallifrey with some of the fellow members of his House. However, he edits Susan out of the memories he shows - technically, he went through the criminal justice system for this, but Susan never did and he doesn't want her to. Gallifrey has seemingly forgotten about her, and he wants to keep it that way.

And then he has his vision trip dream sequence where he sees the past and sees the Timeless Child walk into the Looms. He then sees a memory of himself meeting Susan. This isn't literal - it's symbolic of Susan and the Doctor's relationship changing and evolving as they left Gallifrey. The Doctor knows this isn't literal, but it's in his best interests to act like it is - he's not in control of this dream sequence and several other people are there (including one of the Doctor's enemies), and he still wants to protect Susan, so he goes along with that story.

The Doctor continues their life and eventually gets to the Thirteenth Doctor where she meets the Fugitive Doctor in Fugitive of the Judoon. When she scans herself and the Fugitive Doctor, the two register as the same entity. However, Time Lords are not biologically identical across regenerations - the Doctor has to have something specific to herself that she is looking for.

And she actually has one. At some point in the Doctor's life, they found a genetic quirk that has persisted across their regenerations. They don't know it, but it's the Yssgaroth Taint. Since the Doctor has never encountered another Time Lord with the Taint, she is by this point assuming it's a quirk of her own biology, so takes her sonic detecting the Taint in the Fugitive Doctor as confirmation that the two are the same.

And then shortly after the Doctor meets her genetic predecessor, the aforementioned stuff with Tecteun happens. It's possible that the Doctor themselves has noted the ambiguities in their backstory and heritage but given that there were several thousand years of life between the Seventh and Thirteenth Doctors, it seems likely that they don't think to try to analyze it that closely.