The Doctor is not present when the guards arrive, and we can only speculate what happens to him next. Maybe he escapes from Gallifrey, and spends the subsequent three incarnations as a fugitive. What is certain is that the Doctor eventually returns to Gallifrey and is born from the Loom of Lungbarrow as the Hartnell incarnation, with little or no memory of having lived before. As far as his cousins are concerned, he's a new person. Perhaps this was imposed upon him as a form of punishment - but in the absence of any contradictory evidence, I prefer to think that the Doctor has done something clever to elude his pursuers. He has regenerated, but arranged things so it appears he's being woven from the Loom. The fact that he still has a navel shows he's really the same womb-born Time Lord as the previous incarnations. (And indeed in Lungbarrow, the young Doctor says that he can remember being in the Loom, waiting to be born, which is dismissed as "impossible".)

However, we cannot dismiss completely the notion that the Time Lords themselves wiped the Doctor's memories and effectively let him be born again as a new person. They certainly seem to have form for this - evidence revealed in The Timeless Children suggests that the Doctor's history may go back much further than we hitherto suspected - maybe even to an origin preceding Gallifrey and the Time Lords - but the veracity and reliabilty of this information is as yet uncertain. Nevertheless, we have seen the suggestion of multiple regenerations.

	We learn that eventually the Doctor will start working for a shadowy Time Lord organization known only as "Division", seemingly through several incarnations - before finally going on the run from her employers. It is this incarnation who, whilst in hiding, crosses paths with the thirteenth Doctor, as we see in Fugitive of the Judoon.

Though the true history has been hidden, overwritten and destroyed, there are strong clues that the Division wiped the Doctor's memories to cover their tracks. But was this the same incident as described above? Or was it perhaps one of several, repeated mind-wipes and resets that have occurred throughout the Doctor's life? We simply don't know yet.
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In an attempt to reconcile all the evidence, I would suggest that this is what is really happening in The Black Hole: The Monk has discovered that the Sontarans are about to attack Space Station Camera and slaughter the crew, so he decides this will make a suitable trap to send the Doctor into. It's made abundantly clear in dialogue that he knew the Sontarans would be there - and as Jamie says: "you sent us there to die!" We can assume the Monk also detects temporal distortions there from the time travel experiments, making it a totally plausible environment into which the Time Lords would send an agent. (What the Monk doesn't know is that the CIA have also spotted what's going on, and are going to send their own agent to look into it - that agent being the "Season 6B" Doctor!) So the Doctor and Jamie set off for Camera at the Monk's behest. When they get there, the Tardis won't allow them to land because it has detected its own future self present on the station. Because both iterations of the Tardis are operating using the remote control systems, we might assume there's some sort of safety protocol that stops them materializing on top of each other. The Doctor then detects the Sontarans about to attack the station, and realizes that it's a trap. He also spots the presence of the future Tardis, and knows he just has to leave his future self to sort it all out. So the Doctor breaks the remote control, and sets off to get himself and Jamie back to the Habitat, via a number of unplanned detours. At the end of The Black Hole, it's implied that (the real) Pavo wipes the Doctor's memory of all that has happened, so neither he or Jamie will remember any of it.

Now, let's jump ahead to World Game. The CIA have instructed the Doctor to go and put a stop to the time travel experiments on Camera. The Doctor asks for Jamie as a companion, which of course means undoing the memory wipe that was done on Jamie at the end of The War Games. I reason that the Doctor doesn't want Jamie to have to go through all the heartbreak of their separation again, so he suggests that the CIA reset Jamie's memory to an earlier time. But when considering which point they should roll Jamie back to, some subconscious memory of The Black Hole comes back to him - the mention of Dastari and Space Station Camera triggering the thought of Victoria studying graphology - so he gives it as the new backstory for Jamie. And so the events of The Two Doctors unfold from there.
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So while the Trevor Martin Doctor carries on as a sort of off-shoot incarnation, the Pertwee Doctor remains behind - still irradiated, still dying. The burst of energy from the bi-generation may have helped to temporarily hold the effects of the radiation at bay, allowing the Doctor to carry on for a while - although there are still clues that all is not well. Perhaps one of the effects is a gradual breakdown of the morphic structure of the Doctor's body - which accounts for why he looks slightly different from normal in The Story of Aladdin. (Other than the fact that stuntman Terry Walsh is standing in for Pertwee here.) And then the deterioration continues. In Ancient Whispers, the now weakened Doctor is unsure of his chances of achieving a successful regeneration without outside assistance. Finally, he can't even operate the Tardis, and has to rely on the ship to bring him back home. (Although in Love and War, we learn that it takes him ten years to finally make it back to UNIT HQ.)

I don't intend to speculate as to whether the Trevor Martin incarnation continues on his own timeline and has further regenerations. As with the David Banks version, I suspect eventually the biodata will be re-absorbed into the Doctor's primary timeline. Maybe the Time Lords get involved to sort things out. After all, they know who the actual fourth Doctor should be - especially since he became President and saved the planet twice, they've got a vested interest in ensuring the Doctor's timeline remains stable.
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The story does seem to be set in a different continuity, one in which the Time Lords are all but extinct. What I find interesting about this is the way it echoes later developments in the Eighth Doctor novels, particularly in the aftermath of The Ancestor Cell, when there are said to be only four Time Lords left alive in the universe - one of whom is the Minister of Chance. It's as if the events of that War in Heaven are so cataclysmic that they have repercussions in the past as well as the future. (In fact, if this had been an eighth Doctor story, I doubt there would have been half as much controversy around it.) So maybe that's what's going on here, future events rippling back and overwriting the established timelines. One presumes that the ending, and the Doctor's defeat of General Tannis, cancels all that out and puts events back on their proper course.

I've placed the story almost at the end of the seventh Doctor's life. This is quite a nebulous period, perhaps a long time after any other recorded adventures of this incarnation, and we may never know what leads to these events. Obviously, the Doctor does not actually die at the end of the story - and it's made quite clear that they never find his body. I believe that he withdraws from circulation following this, and keeps a deliberately low profile. (Doom Coalition suggests that the Doctor turns into a sort of errand boy for the President; and in his final days, he appears quite low key and introspective.)
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There's been a tendency to seize upon almost any moment when the Doctor is temporarily without his companions to crowbar in any number of adventures - but my personal belief is that the Doctor would not willingly leave his current companion(s) behind for extended periods. (Except on those rare occasions when we're told in the narrative itself that he has. So for instance, we know he leaves Sam for a while prior to Vampire Science, and this might seem the ideal place to put the early comic strips and audios. However, my personal feeling is that this "gap" is too early in the eighth Doctor's life for some of these cataclysmic events to be occurring - the whole Universe being rebooted for instance.) So I made an arbitrary decision to break the novel series after Interference. I felt that the structure of the novel actually supported this: it starts with the Doctor travelling alone, and the main body of the story is a flashback - by the end of which, Sam has left him and Fitz is dead. True, he's being recreated by the Tardis's memory banks, but that's where the story ends. Does Fitz need time to recuperate from this process? Another interesting point is that we don't see any moment in Interference when Compassion actually becomes a companion - indeed in the framing story, when Foreman asks the Doctor what he did with her, he side-steps the issue. In the next novel the Doctor, Fitz and Compassion are simply depicted as the current Tardis crew, but the formation of that team is something we don't see happen - so I maintain that there is some latitude to play with there. It fits with my schema of dividing the stories into the arcs of different companions. Interference definitely ends Sam's arc, and The Blue Angel can be seen as the start of a new arc about Compassion.

Now don't get me wrong: I'm aware that this is not an ideal solution, but it created a structure that worked for Complete Adventures, and to my mind, is still the most satisfying way of doing it. I don't think it's any more unreasonable than some of the places where Big Finish have crowbarred years of adventures between two seemingly contiguous tv stories. On the other hand, if one is only following the novels, then they can still be read as a continuing narrative. Of course, I should note that I devised all this before the new tv series started. It's now obvious that Gallifrey must be restored at some point following the events of The Gallifrey Chronicles - so that it's there to be "destroyed" again during the Time War! - so one could place the audios and comics after the novels if one so desired. The trouble there is that both End Game and Storm Warning feel like the starting points of "early" series of adventures - it's certainly difficult to conceive of either series picking up after the events of The Gallifrey Chronicles - so overall I'd still like them to go somewhere before the destruction and restoration of Gallifrey.
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Of course, a different version of the same adventure occurring to more than one Doctor is nothing new. I've already dealt with The Ultimate Adventure, Shada and the redrawn TV Comic strips. As with those, I'd suggest that the Doctor is drawn on some subconscious level towards such areas of quantum instability, as if feeling the need to restore missing sections of his timeline. Alternatively, it may be that the Tardis is deliberately seeking out these space-time discontinuities. After all, when the Doctor activates the chameleon arch, he leaves all the details to the Tardis: creating a credible backstory and finding the right setting for the John Smith schoolmaster persona. Though the Doctor may not himself recall the events of the original Human Nature, we can imagine that the Tardis on some quantum level retains that knowledge in its memory banks, and automatically draws upon it to create the Doctor's new human form; and in locating a setting in which to place him, homes in on an area of quantum instability to try and protect the integrity of the Doctor's timeline.
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