Doctor Who/WMG/Classic Series

Specific speculation on the Eccleston era onward goes into

Specific speculation on the latest series goes into (contains spoilers).

Archived Jossed speculation for the final Tennant years post-"Last of the Time Lords" is in

Specific speculation of Matt Smith's first series goes into

General speculation on Doctor Who goes into.

The War Chief is a prior regeneration of the Master.
A renegade Time Lord himself, the War Chief's modus operandi is almost identical to the Master's: form an alliance for power with a very powerful alien race, bringing time travel technology and hypnosis to the table.

This idea has been pretty entrenched and has a lot of history behind it. In fact, the roleplaying game assumed the War Chief and the Master were one and the same.

Zoe is a descendant of sherlock holmes.

 * Isn't Sherlock Holmes a fictional person in the Whoniverse?
 * No Holmes appeared in "All-Consuming Fire" and Mycroft apperd in "The Adventure of the Diogenes Damsel"

Susan is either three-quarters human or three-quarters Time Lord.
Assuming that Susan's grandmother was never mentioned in the old series, and given the unreliability of the Expanded Universe, it is entirely possible that Susan's grandmother was human seeing as how human beings have been stated to be the Doctor's favorite species. The "three-quarters" part comes from the fact that the Doctor's child may have married either a human or a Time Lord.
 * Possibly Jossed by Ten's claim that there's never been a half-human Time Lord, making the first part of this WMG impossible.

The fifth Doctor is the final incarnation of the original Doctor. The Sixth Doctor is a reincarnation, and the beginning of a new 13 body lifecycle.
In The Brain Of Morbius, we are introduced to several of the Doctor's before the first. If these are to be believed, then the fourth Doctor is actually the twelfth Doctor, and the fifth Doctor is the thirteenth. This is why his regeneration ends with him claiming "it feels different this time", and why the sixth Doctor has such a hard time trying to settle down: because he's just reincarnated into a new lifecycle, and he's essentially been reset to his factory settings. No wonder his mind is a bit boggled -- he's actually a brand new first Doctor.
 * The First Doctor is definitively and officially the first (as he explicitly mentions in The Five Doctors), with no prior regenerations. On the other hand, there may be more than one "First Doctor."
 * He says that he is the original Doctor. The First Doctor. But he wasn't always called the Doctor...
 * This seems unlikely, given that the Eleventh Doctor explicitly tells Craig "Eleventh" in The Lodger.
 * I've heard it argued the other heads seen in the battle weren't the Doctor's, but were actually Morbius's.
 * Or, if this is correct, think of The Two Doctors. There was possibly a time between The War Games and Spearhead from Space, where the Doctor could have regenerated any number of times, and the one in The War Games was fake (think of Devious). And there's the time between Doctor Who and Rose. If this is true:
 * One is One, Two is Two, Three is Eleven, Four is Twelve, Five is Thirteen, Six is One, Seven is Two, Eight is Three, Nine is Nine, Ten is Ten, and Eleven is Eleven. Any objections?

The Missing Episodes are missing because of the Time Lords wiping Jamie's and Zoe's memories of their adventures with the Doctor.
They are quite thorough, you see.
 * The reason a number of them are being found is because, thanks to The Great Time War, everything that the Time Lords have done is being reversed or falling apart.
 * Unfortunately for this theory, the majority all but one of the complete Second Doctor serials are from the Jamie/Zoe season. And it wouldn't account for the loss of episodes from before Jamie joined.
 * Time war. It explains everything. Thanks, Russell!
 * [[media:Gallifrey_time_war.jpg|I just had to.]]
 * Wait - does this mean that the Time War was caused by Superboy Prime punching history, or was Superboy Prime caused by the Time War?
 * The Time Lords specifically preserved their first encounter of The Doctor, thus giving an illusion that The Doctor came to them but they never went with him. At the time of writing this -- 23/XI/2009 -- not a frame of footage from "The Highlanders" (Jamie's debut) survives.
 * Repeat -- the Time War explains everything. The Time Lords preserved that episode, not us -- and the Doctor wiped the Time Lords out. Multiple times.

The Time Lords screwed up and wiped everyone's memories except Jamie and Zoe's.
Fixes the problems with the above theory.

The Missing Episodes are missing because the Doctor accidentally wiped them.
One's regeneration had suspiciously few side effects. Instead of his getting direct amnesia (which would happen a lot to the Doctor later), he wiped many of the records of his adventures telepathically. (Most of the ones with Susan survived because she was a Time Lady.)

Two wiped his records telepathically the same way, but Jamie was a stabilizing influence. If Two hadn't met Jamie, we would have no more televised records of his adventures than we have televised records of Eight's.

"Dr. Who And The Daleks" is a TV show in the Doctor Who and Buffy the Vampire Slayer worlds.
First, we must combine four pieces of information:


 * 1) Due to (among another things) a cameo by The Doctor and Rose in the Buffy comic, the two shows take place in the same universe. (See this page for more info).
 * 2) In the Buffy episode "Smashed", Andrew says that he's seen "every episode of Doctor Who" on DVD. Now, this sounds contradictory with #1. But remember that it's impossible for him to have seen every episode on DVD: Not only are there missing episodes, but the reconstructions of said episodes by Loose Cannon Productions are only available on VHS. So it can't be the Doctor Who we all know and love.
 * 3) The Doctor Who episode "Rememberance Of The Daleks" has an announcer on TV introduce an episode of "Doctor Who". But again, it can't be the Doctor Who for obvious reasons.
 * 4) John Peel, who novelized most of the early Dalek serials, states in his book that in the Doctor Who universe, the movie "Dr. Who And The Daleks" was created by Barbara Wright as a way of making some money from her adventures and alerting people to the existence of the Daleks, without giving away too much about the real Doctor.

Now, all of this creates a gigantic timey-wimey ball of contradictory canon weirdness. But wait!

So, in the Doctor Who universe there's a movie and TV show called "Dr. Who". Now, the movie "Dr. Who And The Daleks" could not have come before the TV show; the people in "Rememberance" didn't recognize the Daleks. So the only possible conclusion is this: In the Buffy/Doctor Who universe, "Dr. Who And The Daleks" was a popular kitsch classic TV show from the mid-1960's that got adapted into two equally kitsch movies. The existence of this hypothetical show cleans up the Fridge Logic that comes with the "Rememberance" sequence and Andrew's "I've seen every episode of Doctor Who" statement.

This may set a record for the largest ever density of Fan Wank. Or would if the Cartmel Masterplan didn't exist.
 * The Protectors of the Plot Continuum mission Hidden Truths, Hidden Lies establishes that the spread of missing episodes varies from universe to universe. It's quite possible that in some 'verses, The BBC never junked a frame. In others, there are missing and B&W episodes right up until the advent and popularization of the VCR (which would mean that only Six and Seven would have complete runs).

In The Verse of Buffy the Vampire Slayer, Doctor Who lasted only one season.
This was threatened in Real Life. And the Buffyverse is usually worse than Real Life.

The Time Lords are the reason the Doctor has regeneration trouble
The Second Doctor had no post-regeneration trauma. The later Doctors all have it. The Time Lords were responsible for forcing the Second Doctor to regenerate into the Third Doctor, and so it's possible a spanner was thrown into the works there.

The First Doctor avoided regeneration trouble because he "died" naturally.
The First Doctor is the only one who died of being "worn out" (the Time Lord equivalent of "natural causes"). Two was forced to regenerate. The rest all died after suffering massive physical trauma (radiation, a violent fall, poisoning, being murdered by Michael Grade, etc...).

Perhaps "dying before your time" -- violently, abruptly, or with major damage -- causes the regeneration to be flawed. Most Time Lords lived long, full lives and viewed regeneration more as rejuvenation (which is how Two describes the process after One changes) then as the emergency survival mechanism all the later incarnations use it as.

In other words, if the Doctor had lived a calmer, less dangerous life, then his regenerations would have gone far smoother.

Hermann (the butler from City of Death) is the Master.
The Butler Did It. It's that simple!

The Fourth Doctor "danced" with Romana.
There's the off-screen relationship between Tom Baker and Lalla Ward, but let's look at the canon evidence. She's a Hot Scientist, she's a Defrosting Ice Queen, she's a Time Lord, and she (in her second incarnation) was a redhead. Since the Doctor has expressed a desire to have red hair himself, it's obvious he fancies redheads.
 * That doesn't explain his second love, the peroxide blonde Rose.
 * He likes both redheads and blondes. By the way, his peroxide blonde count stands at two, with Madame de Pompadour as number two. (Incidentally, the Real Life Madame de Pompadour wasn't a peroxide blonde, judging by her portraits. Perhaps the production team stuck with Sophia Myles' adopted hair colour because it would add to the "courtesan" image -- peroxide blonde hair spent a considerable amount of time being associated with the oldest profession.)
 * There's Astrid, too. Another blonde.
 * The Doctor and the first Romana also had a Slap Slap Kiss thing going on.
 * Well, given how according to Moffat, the Doctor can only reveal his name to his spouse, and given how the second line Romana I said was "My name is Romanadvoratrelundar..."

The Time Lady that Leela bumps into in "The Invasion of Time" is an earlier regeneration of Romana.
Rodan changed her name and regenerated because she was afraid that she'd get into trouble for her part in the invasion: she knows exactly how corrupt timelord society is and didn't want to take any chances.

The producers of the show invented the character of Romana after the actress who played Rudan (Hilary Ryan) was unavailable, so this fits quite well.

It also explains why the White Guardian picked her to accompany the doctor, as she had proved herself already. As to why she doesn't tell the Doctor, it's possible that her memories of the invasion were wiped for extra protection.

Season 6B
This theory, being a widespread fan theory, itself belongs in WMG even though it was around long before TV Tropes.org. At the end of the Second Doctor's last story, "The War Games", companions Jamie and Zoe are sent back to their own times with memory wipes, and the Time Lords force him to regenerate into the Third Doctor and send him to Earth.

However, in "The Five Doctors", the Second Doctor recognizes illusions of them as fake because the illusions recognize the Brigadier, while the real ones had their memories of him wiped. This shouldn't happen; he regenerated right after those memory wipes, so he shouldn't know about them and still be the Second Doctor. Moreover, in "The Two Doctors", Jamie and the Doctor are on a mission for the Time Lords, even though Jamie didn't even know about the Time Lords until "The War Games" - which was the Second Doctor's and Jamie's last serial if Season 6B isn't true.

The 6B theory is that the last episode of "The War Games" has many stories crammed in between the memory wipe and the regeneration (which we see at most half of), during which the Doctor was working as an agent for the Time Lords. The theory originates with Paul Cornell, who would later write Doctor Who novels and audios and has written for the show itself in the new series.

There is other evidence for 6B in-series. In The Three Doctors, Two is brought over without any companions. But he always had a companion during his original run until the Time Lords took them away in the last serial. He started with Ben and Polly; and once he met Jamie, the pair stuck together.

And in "The Two Doctors," there are two difficulties that can only be explained In-Universe by 6B. One is that both Two and Jamie have aged a lot from Two's original. Mind you, Time Lords live a long time; Two physically aging (he has grey hair, even) means that he probably spent a few centuries adventuring alone.

The other is that Two in "The Two Doctors" has a remote controlled TARDIS -- something no Doctor has had before or since. Six is jealous of it, even. But during his run, Two had no control over where his TARDIS went at all. The remote control was clearly provided by the CIA. It was removed when Two finally was turned into Three -- the TARDIS was sent to earth with him in non-working order, so the remote control was removed with all the other working parts.


 * It can get convoluted. For instance, there's a reference in "The Two Doctors" to Victoria being temporarily away, which is obviously meant to imply that the Doctor and Jamie were from the Jamie/Victoria era and that this is why Victoria isn't in the story. If they're from season 6B, the Doctor must have picked up Victoria again just so that the story can explain why she's not there.
 * On the other hand, the Doctor had absolutely no control over the TARDIS during the period when he traveled with Victoria, so the idea of having dropped her off somewhere (before Season 6B) with the intention of coming back for her seems unlikely.
 * In some variants of the theory, Victoria didn't rejoin the TARDIS; rather, Jamie thought she should be there because of all the tampering that's been done to his memory. This is the case in World Game, for example.
 * The "Five Doctors" scene doesn't make sense even if 6B explains why the Doctor knew about the mind wipe. Jamie and Zoe could have been taken from a time period before their memories were wiped -- it just isn't correct to conclude that not having their minds wiped means they must be fakes.
 * It doesn't matter if Two's reasoning in "The Five Doctors" is valid; what matters is, he knew about the mind wipe! It doesn't matter that Jamie and Zoe could have been scooped out from before "The Invasion"; what matters is that Two believes that they would have taken after a mindwipe that, without Season 6B, would've happened shortly before Two ceased to be Two. Someone scooped him out from under the noses of the Gallifreyan justice system; it's better if that someone is the CIA.
 * Note that the Second Doctor can SEE that both Jamie and Zoe are clearly a bit older than they were when the Time Lords sent them home, and thus knows that they absolutely MUST come from a time post-mindwipe. And he himself is clearly older than he was during the tribunal -- which would strongly imply a time after the tribunal, which is impossible without Season 6B.
 * In "The War Games" itself, it seems obvious that the scenes happened at the same time.
 * The usual explanation for this is that we don't see the Doctor change--we see at most half a regeneration--and he was rescued by the CIA at the last second, leaving the tribunal to think that sentence had been carried out. Perhaps the CIA stalled his regeneration, just like Ten stopped himself from turning into Eleven.
 * This is canon in some parts of the Expanded Universe: back in '69-70, the comic strip saw the Second Doctor begin the exile on Earth, only later having his face changed by sentient scarecrows. Terrance Dicks has also written a novel -- World Game -- that has the Second Doctor as an agent of the Celestial Intervention Agency after "The War Games" and setting up his appearance in The Two Doctors as well.

The Valeyard is the Second Doctor from "The Two Doctors".
Never mind Season 6b. The reason that the Second Doctor in "The Two Doctors" looks older is because he's a Second Doctor from an alternate universe who was brought into our universe by the Celestial Intervention Agency to act as their agent because "their" Doctor refused to. They allow Jamie and Victoria to go along with him, but they eventually die of old age (Jamie is noticeably older in "The Two Doctors"), and the Alternate Doctor goes through the rest of his regenerations in quick succession thanks to the dangerous missions the CIA keep sending him into, hence the Valeyard being "somewhere between [the Doctor's] twelfth and final incarnations." He literally is one of the Doctor's future selves, just an alternate one. He eventually becomes bitter and twisted as a result of his enforced slavery - in fact, as early as "The Two Doctors", you can sort of see it happening. To mollify him, the CIA eventually agreed to give him the remaining regenerations of the "real" Doctor and allow him to take the Doctor's place in our universe - hence the trial.

You know it makes sense.
 * But then why would the Second Doctor's transformation into an Androgum in "The Two Doctors" threaten to eventually affect the Sixth Doctor? That only makes sense if they're two parts of the same lifespan.
 * Because the alternate Second Doctor and the Sixth Doctor still share a psychic link; they are 'almost' the same man, and one could still be the predecessor of the other (the alternate Second Doctor could still have a sixth incarnation who looks and appears to be almost exactly like the Sixth Doctor we know and love), so they're almost identical to each other, except one comes from a slightly different alternate universe. As such, the alternative Second Doctor's androgum transformation still affects the Sixth Doctor psychically, but he confuses this with it altering his past. He isn't actually becoming an Androgum, but is psychically convinced that he is.

Zoe is not what she seems.
Space Station W3 (The Wheel in Space) is an artificial universe like Castrovalva, and all its crew, including Zoe, are either constructs like Shardovan and Mergrave or in on the scam.

Rationale: None of the Wheel's occupants find it extraordinary that the Cybermen, so down on their luck that they can't take over the Wheel except by stealth, can cause local meteor storms by setting off novas 25,100 lightyears away (and therefore 25,100 years ago). The Cybermen can set off the novas because the stars around the Wheel are really very close and attached to the inner surface of a crystal globe where the Cybermen can get at them. No-one on the Wheel seems to notice this. Either they can't perceive the impossibility, just as the Castrovalvans couldn't perceive the logical flaws in their environment, or they know it's impossible but see no need for the Doctor to know that.

Following this train of thought leads to the conclusion that the pocket universe existed to get Zoe on board the TARDIS and that she was a conscious or unconscious agent for whoever set the thing up, be it the Celestial Toymaker, one of the Guardians, or the CIA.

If it's the CIA, then this is a timeline without Season 6B, and the Second Doctor's part of "The Two Doctors" happened some time in Season 5. Zoe would be a chameleon-arched Time Lord. Perhaps she was created from a Time Lady called Zodin.
 * Also, Shardovan destroying Castrovalva could explain why Zoe's "2000" isn't our "2000". Castrovalva's destruction meant that that world (which was created by the Master) could never become the Space Wheel and, thus, that Zoe's timeline never happened. But, since it happened in the Doctor's past, Zoe still existed when she was with the Doctor. This would mean that the Master set this up to use Zoe as his agent. Zoe joined the Tardis to force Two into "The War Games" so that he would (eventually) become Three. That way, Three would be there, trapped on Earth without a working TARDIS, when the Delgado Master kept trying to take over the Earth. Fans of the new series already know that the Master likes to mix the Doctor into his plans...

The destruction of Shardovan is why there are so many missing episodes
The Doctor had few run-ins with Time Lords between when Susan left and when Two was forced to regenerate. Since the Wheel in Space is directly related to a pocket universe created by a Time Lord, the presence of a resident of this place as his companion helped stabilize the records. But, since the place ceased to exist in its own timeline before Zoe could be born, much of the Doctor's personal history prior to the Space Wheel is recorded only in fragments, especially when the Doctor was the only Time Lord in the area.

The Master's final death was in "Planet of Fire".
From the Master's personal chronology, he first fought the Doctor in several offscreen encounters with the First and Second Doctors. He was, at one point, in conflict with Skaro and executed there, but they granted his request to be taken back to Gallifrey by the Doctor, with the events of the Made for TV Movie taking place for him before having met Doctors 3-6. He was resurrected by the Time Lords to fight in the war, and ran off to the end of the universe, where he hid until the Doctor arrived in Utopia. Sometime after the end of Season 3, he ran away to 1970s Earth, where his and the Doctor's meetings happened more or less in order, until he met the sixth Doctor twice and the seventh once before finally dying at the end of "Planet of Fire".

The Master is killed in every episode he appears.
Every time we see the Master, it's an earlier version. The Doctor keeps killing him at earlier and earlier stages in his life, creating more and more paradoxes.
 * This would explain his Villain Decay; he's actually getting more and more badass, we're just seeing it all in reverse order.
 * The drums were eventually blocked when he grew a goatee.

Time Lord names are bestowed at initiation, and hence have ceremonial significance; anonymity is thus a universal mark of Time Lord rebellion.
The Doctor, The Master, the Meddling Monk, the War Chief, the Rani... it certainly seems that once you leave Gallifrey, you lose your name; even the otherwise most iconoclastic Time Lords feel this to be appropriate. Romana would seem to be an exception, but she began her journeys with the Doctor thinking she was doing the business of Gallifrey; it's possible she changed to a suitably anonymous moniker (as in the BBV audio plays with "K9 and Mistress") once she made the decision to abandon Gallifrey of her own accord and remain in E-space.

The Doctor is part human by way of Stable Time Loop.
A love affair between Susan Foreman and Captain Jack Harkness in the 22nd century created a hybrid bloodline, which culminated in a mostly human time traveler who would come to be known as the Other. The Other somehow ended up in Gallifrey's distant past, and was subsequently reincarnated as the current Doctor. So his soul is part human, anyway...
 * That makes it squicky that Jack kissed the Doctor. Then again, with his sexual appetite and the Timey-Wimey Ball, Jack has probably snogged many distant relatives by now. Perhaps a few closer ones as well in his original century.

Sutekh the Destroyer (from "Pyramids of Mars") is aware of the Beast (from "The Impossible Planet"/"The Satan Pit") and is consciously imitating him.
He goes by the name "Satan" and sounds like Gabriel Woolf. That can't be coincidence. Since the Osirians are a bunch of Ancient Astronauts posing as gods, it's likely Sutekh decided to take the identity of an even more Sufficiently Advanced Alien that fitted his place in the pantheon.
 * Somewhat like the Daemons, you mean?
 * Isn't there a line in "The Impossible Planet/The Satan Pit" where the Doctor mentions the various races who have taken on the characteristics of gods and demons (Like the Daemons and the Osirans), and the Beast claims to have inspired them all? Sutekh and his race may be acting on some race memory in adopting a simmilar MO. They may even be related to the Beast and his species (such as his "Son" who showed up in Torchwood series 1), or literally inspired by him.

Everything after the end of "Trial of a Time Lord" takes place in the Matrix.
At the end of "Trial of a Time Lord", the Doctor pops up from out of nowhere, having staged a miraculous escape from the Matrix as it was imploding after a battle with his Evil Dark Half, The Valeyard. He then leaves with his companion Mel, bidding the Inquisitor at his trial a warm farewell and suggesting that she should run for President -- and as he's leaving, the Valeyard turns around, disguised as a minor character called the Keeper of the Matrix, and chuckles sinisterly...

Hold on, hold on, hold on. There's more than a few things wrong with this picture:
 * 1) Where did the Doctor come from?
 * 2) Why is he leaving with Mel -- a companion who he hasn't even met yet (owing to complicated Timey-Wimey Ball reasons)?
 * 3) Why would he be inclined to wish the Inquisitor well at all, much less suggest that he'd vote for her? The woman just presided over a Kangaroo Court whose sole purpose was to shop him to disguise the crimes of the Time Lords in destroying Earth to protect their secrets. The Doctor -- the Sixth Doctor particularly -- isn't that forgiving, especially since less than an episode earlier, he'd been angrily berating the Time Lords for their corruption.
 * 4) The Valeyard was last seen dying... somehow... in the Matrix. How did he escape? How did he take over the Keeper's body? And how come no one has noticed that the Keeper now looks like a totally different man (a younger and taller one for a start) and, in fact, looks exactly like the Valeyard?

Possible solution -- the Doctor didn't escape from the Matrix. He's still in there. The rest of the series was a Lotus Eater Machine Dream stage--managed by the Valeyard to torment him. The illogical ending of the series (including his final battle with the Valeyard, involving Megabyte Modems and such) was a ruse to convince the Doctor that he had won so he wouldn't question his new environment and try to escape.

This explains a fair bit about the rest of series. The Sixth Doctor's curiously unexplained regeneration? Forced by the Valeyard as part of his torture. The Seventh Doctor's Character Development from cheeky little Scots chappie to angsty, tortured Time's Champion? The Valeyard making the Doctor's life increasingly difficult and complex. We can even bring in the new series if we want -- what better way to torture the Doctor than make him think he's blown up his own planet and committed genocide against his own kind and, to rub this in, making the only thing that would possibly make this atrocity worthwhile -- wiping out the Daleks at the same time -- a hollow victory by constantly bringing them back to face him? The Doctor hasn't done any of these things; in fact, he possibly hasn't even regenerated, and what we think is the new series is a fantasy concocted in the mind of the trapped Sixth Doctor as he floats in the Matrix, trying to work out where he is.

Or, you know, possibly not.
 * Also, the Doctor's (which has numerous gaping logical holes in it) in "Journey's End" could be the Valeyard . After six more, the Valeyard will.
 * It looks like

The First Doctor is not the "First" Doctor.
The Doctor could have had one or two regenerations before the first episode of the series. ""I am the Doctor, the original, you might say!""
 * Jossed by "The Five Doctors":


 * But hinted at in "The Brain of Morbius", in the mind-battle thing that the Doctor fights Morbius in; after the Doctor's first four selves a lot of faces we don't recognize appear, and as the Doctor seems to be losing that battle it seems heavily implied that they're previous incarnations of him. Ah, the wonders of Doctor Who and consistent continuity...
 * It has been suggested that the other faces were those of the Doctor's past reincarnation known as the Other (from Virgin's line of books). Alternatively, the other faces were Morbius's.

The One we know from his original run was Two(a) left in a chameleon arch too long.
"One" always wore a special ring that could open the Tardis. Two proved he wasn't One by showing that the ring no longer fit, and it was never used again. "One"'s death by old age released Two(a) from the arch.

We do see the real One in "The Five Doctors", and he does look and act similar to the "One" of the original run. But he's not quite the same.

This is why, in "The Three Doctors," "One" is forced to teleconference. The CIA tried to pull the wrong "One" into the scene, and the Blinovitch Limitation Effect wouldn't allow an extra Two in the immediate area, even if he looked like One.

Rose Tyler is one of the Wolves of Fenric.
The Wolves of Fenric were introduced in the original series episode "The Curse of Fenric". In that serial, various descendents of Viking settlers were touched by the titular Curse, which made them psychically suggestable and also connected to the Vortex (it is this that enabled Ace to accidentally create a Time Rift with a chemistry set). Rose can open her mind to the "heart of the TARDIS", ride the powers of the Vortex and become "the Bad Wolf".
 * Not only that, but the rest of her family line (and, therefore, Wolves of Fenric) includes precognative Martha Tyler (from the original series serial "Image of the Fendahl"), time traveler Sam Tyler (Life On Mars), "magic" user and time traveler Stephen Tyler (CBBC drama The Magician's House), powerful psychic Gabriel Tyler (DW Expanded Universe novel Damaged Goods by Russell T. Davies) and demon-posessed Johnny Tyler (Second Coming, an ITV serial also by Davies).

Romana's soul is connected to Smith's watch.
There was a female voice in the watch, a major part of Latimer's inspiration. Since the Rani, the other major female Time Lord in the series, does not go about inspiring human schoolboys to greatness, and since Romana has already demonstrated her love for the trappings of public schools, is it possible that the Chameleon Arc served as a portal to a pocket-world containing the souls of multiple Time Lords?
 * According to the writers, had the seventh Doctor continued without being cancelled, his companion Ace would have eventually joined the Academy to become a Time Lord. The novels with the Seventh Doctor aren't continuity, so her fate is currently unknown. Just a thought...
 * RTD and others have said that they don't consider the novels out of continuity; he just doesn't plan to make them explicitly part of canon either. So with no Word of God to confirm or deny how canonical the books are, it's up to Fanon for the foreseeable future.

Time Lords regenerate into different people so they can safely meet themselves when travelling through time.
In "Father's Day," it's implied -- and to some extent shown -- that nasty things happen when you meet yourself. But in "The nth Doctors" specials, The Doctor doesn't seem to have this problem, or at least not as badly. (It just tends to temporarily age the earlier incarnation.) The regeneration mechanism was purposely designed with this in mind.
 * In "The Three Doctors," it is implied that it takes a great deal of energy to break the First Law of Time in this fashion. This may be a property of TARDIS travel, however - a safety feature, as it were. In "The Five Doctors," a Time Scoop is used to break the First Law of Time, and no one's especially fussed.
 * Breaking the First Law of Time can happen accidentally. It may have happened accidentally in "The Two Doctors" - Six didn't go to Seville specifically to rescue Two and Jamie, and Two certainly wasn't told his future self would be there.

The Doctor was being metaphorical when he said he was half-human.
Let's face it, he's saved Earth specifically how many times? How many of his companions were humans? And he's probably dealt with the Earth many more times offscreen? He meant it in an affectionate way, not a literal way.
 * However, being half human was not just a line of dialog, but a plot point--a human eye was needed to open the Eye of Harmony.
 * Clearly, that jibe of Eight's about the half-broken chameleon arch is true...
 * Wouldn't a Half-Human Hybrid have an eye that's also a hybrid, and thus he wouldn't have a human eye? My solution is that, when he regenerated, he absorbed nearby human DNA. Or some other regeneration mishap altered his biology.
 * If the Doctor was just being metaphorical, why would he have said he was half-human on his mother's side?
 * As a joke. Mother Earth, anyone?
 * He had a flash of precognition to the events of Journey's End. He was still confused and having trouble with his identity, and saw a brief image of his future self, the one that grew from his hand. That Doctor was indeed half human. And the source human half? Donna Noble, making her his "mother".
 * We learn in Voyage of the Damned that he edged out descendants of David the Great for the last room in an in Judean inn. As this troper understands things, that did not happen unless you were a Roman citizen and/or descended from David yourself. Since the Doctor is not a Roman citizen, this means that his mother was a Human who had turned Gallifreyan somehow.

The Doctor represents the Superego, the Rani is the Ego and the Master is the Id.
Think about it! The first Master was going to be written off the show by having him be revealed to be the Id to the Doctor's Ego, but that doesn't quite work. (A corrupted version of this story is where all those brotherhood rumors come from.) The Freudian brain is made up of three parts, not two, and the Doctor is far more a representation of morality than of logic, especially lately. The Master is driven by pure self-interest, and the Rani is coldly logical to the point of amorality. Just imagine a scenario back on Gallifrey where the Doctor and the Master are arguing over something the Master wants to do that the Doctor doesn't approve of, and the ever-exasperated Rani has to mediate a compromise. Works, doesn't it?

This theory has some Unfortunate Implications: it implies that each of them is dysfunctional without the other two. That's not that far off. The Master is already insane and out of control, the Rani is a merciless tyrant, and the Doctor himself can teeter along the edge of Well-Intentioned Extremist-style spookiness if there's no one to hold him back. In fact, the Doctor seems sanest during the season three finale when he has the Master to bounce off of and use for comparison. This also makes shipping any of them with each other even weirder than it already is.
 * Corollary: Life On Mars and Doctor Who take place in the same universe, only Life On Mars is a level down.
 * Specify please - New Who S3, not Old Who, (i.e. Ten, not One) yes?
 * All three of them are archetypes who change slightly based on trauma/experience/growth etc. just like in an actual psyche. That's regeneration. The trio from any one time period "fit" each other. So yes, both old and new Who. Or did you mean which season 3? In that case, yes, Ten, because the Master didn't show up in the classic series until Three's era. Unless you think the War Chief is the Master, but that's a whole different WMG.

Timelords use Regeneration to diversify their gene pool
Space and Time may be open to them, but when you're practically immortal, there's plenty of downtime to go "dancing". While the canonicity of Timelord sexual reproduction is widely debated, if the natives of Gallifrey do sexually reproduce, then they likely developed regeneration so that their offspring can avoid an incest taboo - their siblings will be genetically different. Then again, if his entire planet is "family", no wonder the Doctor spends so much time on Earth and has trouble giving more emotion than "just a handshake" to his companions in the original series.

The Seventh Doctor (Sylvester McCoy) provided the inspiration for the WWI soldier's song "Smile Smile Smile."
You have seen the lyrics, right? He wound up in the trenches through some time-shenanigan or other and wound up temporarily joining with a platoon (in a non-combat capacity), and he doubtless saved everyone nearby from all the exploding nastiness you get in a war at least once.

The Doctor featured in The Movie wasn't number 7 into number 8
Rather, he was 10.5, regenerated. At some point in the future, half-human 10.5 regenerates into a form remarkably similar to the seventh doctor and gets through the Time Lock because he already had. This "remarkably similar to the seventh" form regenerates into what we know as 8 during the movie and vanished- perhaps dying in the Time War. As for the main Doctor, we never see his eighth incarnation, which began and ended during the course of the war.
 * Doctor 10.5 said that he couldn't regenerate.
 * If the 'real' doctor can be wrong, the half-human one definitely can.
 * The reason 10.5 had only one heart and the "remarkably similar to the seventh" form has two is, a Time Lord only grows their second heart when they regenerate for the first time. (This is a well-known theory.) Also, the reason the movie Doctor says he is half human is that he is half-human. 'On his mother's side' is referring to Donna's contributing the human half.
 * It's been confirmed on the show that the Eighth Doctor in the movie was a previous incarnation of the REAL 10th Doctor, not the 10.5 model.
 * Nonononono, It's been confirmed that the Doctor's Eighth Incarnation bears an astonishing resemblance to the Doctor seen in the TV movie. Nothing more, nothing less.

Davros' deformation and omnicidal tendencies can be traced back to an incident involving rice pudding.
The Seventh Doctor clearly struck a nerve in Remembrance of the Daleks.

The Eighth Doctor's Big Finish adventures with Lucie Miller lead directly to his regeneration
It was cut from the final broadcast, but it's generally accepted that Tenth has an Estury accent because he picked up Rose's. So obviously, Ninth's accent indicates that the last person Eighth was talking to regularly was from Oop North. And the most likely candidate is Blackpool-accented Lucie.
 * So when was Seven hanging around with Liverpudlians?
 * There's Hex, but the timing isn't right. Eight should have had Benny's accent or Chris Cwej's (whatever that accent would be). Come to think of it, Six didn't have any Scottish companions, did he?
 * Seven must have loved Hex. And Six knew Jamie McCrimmon, if only briefly.
 * We don't see the adventure that led up to Six's regeneration, so it could easily have been one with Six, Mel, and Jamie. Hopefully one in which Six and Mel went back to Culloden to rescue Jamie and restore his memories.

The Master and The Rani are Jamie and Zoe
Jamie and Zoe were becoming progressively more fixated on the wonders of the universe, and the Time Lords figured out who they were. They knew they had to keep these two from the universe as long as possible and, hopefully, keep them human; so they wiped their memories, separated them from the Doctor, and put them back on Earth. Please note that the Time Lords never did anything similar to any other companion of the Doctor, so it is highly likely they had particular reason to fear Jamie and Zoe. For now, the Doctor is still Two and is just kept in Time Lord jail.

This does not work, as the two are still haunted by subconscious memories of travelling with the Doctor; the Time Lords detect this has a destabilising affect on the Doctor, the universe, Gallifrey, and Jamie and Zoe - their memories get murkier and murkier, detecting things from all sorts of timelines, and the Time Lords start to fear them uncovering their true identities. So the Time Lords pull them back and make them travel with the Doctor, doing what the Time Lords want them to do, but they make sure to keep Zoe and Jamie separate - they travel with the Doctor at separate times, and Jamie gets a human guardian - Victoria, whose memory is edited to make her think that she never stopped travelling with them (or wanting to). Zoe may get her own human guardian. The Doctor knows that the Time Lords are preoccupied with Jamie and Zoe, but doesn't know why, and he eventually pulls the plug on the whole thing by refusing to travel anymore. The Time Lords are absolutely furious with the Doctor, since he might be creating two mass-murdering megalomaniacs, which is why they banish him to Earth and make him regenerate - they take away a significant portion of his life and then do more, a surprisingly harsh sentence.

But it is done, and there is still the question of Jamie and Zoe. They decide to start fresh, regressing their ages (or making them regenarate into babies, one or the other) and sending them back to be contemporaries with the young first Doctor. They all meet and become friends as young children, and the Time Lords forget about it - if there's no famous Doctor in their time, what's going to introduce Jamie and Zoe, who now use other names (say, X for Jamie and Y for Zoe) to the universe, providing everyone keeps to the rules? All predictions on them as children say that they probably will follow the rules.

But the mind-wiped-ness is not as stable as hoped, and when X and Y turn 8 and look into the fabric of space time, all hell breaks loose. X and Y now have subconscious memories of being Jamie and Zoe, and this affects them differently - both become subconsciously angry at the Doctor for not being the Doctor they know. Y turns to knowledge, science and being a genius again. X tries to push the Doctor into being the 'hero' by being the 'villain'. Also, all the time changing and identity shifts have given X and Y issues with their identities, and they create new names, or titles - 'The Master' and 'The Rani'.

Twelve regenerations isn't a physical limit; it's a legal limit
The Time Lords are able to regenerate forever; however, this created a huge population problem. Therefore, the Gallifreyan government imposed a strict twelve-regeneration limit. It's clear that Time Lords can voluntarily NOT regenerate (as the Master showed), and this was made compulsory for Time Lords who have lived out all thirteen lives. However, with the Time Lords gone, there's no-one to enforce the law any more; the Doctor can regenerate as many times as he likes.

Every story after "The Mind Robber" is just dreams of the Doctor -- just fiction.
Recently suggested by The Doctor Who Magazine. At the start of the next serial "The Invasion", the TARDIS is shown reforming (after falling apart during the previous serial). Jamie wakes the Doctor up saying the emergency unit has worked and Zoe then asks if they are on their way anywhere, or if they are stuck (in nowhere). The TARDIS reforming scene is supposed to show that the entirety of "The Mind Robber" took place in the Doctor's mind; but what if the Doctor is still stuck in The Land Of Fiction, and his victory against The Master of The Land Of Fiction was a ruse to make him think he'd won?

Susan is the Doctor's granddaughter... and also the granddaughter of Jack Harkness.
In "Everything Changes", the first episode of Torchwood, Jack mentions that he was pregnant once and is trying to never be again. (Cue Ianto.) The other parent was Nine. The child will go on to produce Susan.
 * You need to stop skipping biology class. His "pregnancy" was probably similar to Gwen's in "Something Borrowed". Also, isn't Susan canonically from Gallifrey? And where did Jack ditch that poor child after it was born? And how did Susan end up with the First Doctor?
 * Yes, Susan is from Gallifrey. Jack ditched her mother somewhere where One would find her. Susan is with One because humans are much shorter-lived than Time Lords, and her mother had the lifespan of a normal human. (Being a fixed point in the universe is not hereditary.)

The Doctor IS half human
That's why he always tries to protect the Earth and praises humanity - obviously, he was mocked for his ancestory as a child, and he feels the need to constantly prove that humans are great. Or else go Spock-like and put them down to prove he's not one of them.

Time Lords only gain their second heart after their first regeneration.
That Three has two hearts is obvious to those at the hospital that took him in, and they didn't cut him open to find out. Seven having two hearts looked and sounded so wrong to Grace, a doctor, that she killed him trying to fix that problem. But Ian Chesterton, a science teacher, thought One was human, and when he listens to One's heartbeat, it sounds normal (read human) to him. Something changed between One and Three; since we are told two hearts are normal for Gallifreyans, the change most likely happened when he regenerated into Two.
 * Two was examined by Gemma Corwyn in "The Wheel in Space" and she didn't notice anything odd about his heartbeat either.
 * See the "Zoe is not what she seems" WMG. The people of the Wheel may have known about Time Lords from the beginning of their recorded history (which begins before their actual history, strangely enough).
 * Alternatively, before the first story, and perhaps before he left Gallifrey in the first place, the Doctor had some medical emergency which, for some reason, required one of his hearts to be removed/disabled. When he regenerated into the Second Doctor, it just got fixed.

Gallifrey is the world of Chrono Trigger.
Gaspar was the first Time Lord, and the End of Times is within his TARDIS.

Not everyone is a Time Lord.
This theory is way-way out there, but it's entirely possible that not every single fictional character ever created is a Time Lord.
 * For example, Vector Prime, as a living machine that can bend the fabric of time and space, is obviously a TARDIS, though probably only because he chose one to transform into.
 * What about the idea that every fictional character is a Time Lord except the Doctor?
 * Obviously. Only some characters are; the rest are companions.
 * Of all the crazy theories floating around here, this is the most absurd!

The first regeneration was a symbol of maturity in Gallifreyans.
Romana regenerates, giving much thought to her form, after the quest for the Key of Time - not because she's hurt, but because she considers herself a mature Gallifreyan. This is why two hearts is considered the default for Gallifreyans - that one-heart stage is childhood. One was rebelling against Gallifrey when he held onto his first form as long as he could (unless he was a chameleon-arched Two(a), in which case all bets are off).

The entire history of the Doctor has been one long game of Xanatos Speed Chess against the creatures of the Cthulhu Mythos
. The Expanded Whoniverse novels not only drew the Old Ones and Endless Ones into the ambiguous canonicity of the novels, but also stated that Rassilon himself named them. The Vortex opening that drove the Master mad was obviously closed after a while because of its connection to the domains of Nyarlathotep and so forth. Each of the Doctor's recurring enemies, as well as many of the one-shots, is connected to one of the more powerful beings - the Daleks to Hastur, some of the more hideous aliens to Shub-Niggurath, and so forth. On an early visit to Earth, the First Doctor found himself on a steam yacht named the Alert and was able to arrange Cthulhu being rammed. Since then, he has been attempting to deal with them however necessary. His death in Turn Left was due to being caught by Deep Ones while regenerating and stabbed in both hearts; through Heroic Willpower and at least one of the regeneration WMGs above, the regeneration limit simply no longer applies, because this is someone who has repeatedly forced the abyss to avert its gaze.

Castrovalva would have become or launched the Wheel in Space if Four hadn't died falling off that radio tower.
Either Four would have avoided going there in the first place, or he would've found a way out that did not involve the residents killing themselves for him. Four likes impossible geometries. Castrovalva, left alone, would have advanced until it had finally launched a space station - with one Zoe Heriot on it...

If the missing episodes ever turn up, then they will be chock full of Fan Service.
Point one: most of the First and Second Doctor episodes that currently exist were rescued because they were in the possession of Arabic countries.

Point two: none of the soundtracks are lost.

So, the episodes that remain missing are missing because they had footage that was offensive to the Arabic countries and so was never shown in them. This would tend to be sexual footage. Most of the Ian-Barbara-Susan-One episodes exist; most of the ones that don't involve medieval Arabs. Episodes with young female travelling companions who aren't related to the Doctor don't fare so well. Polly was a swinger, and most of her episodes are lost; the only Ben-Polly-One episodes that survive are set in Antarctica, and by the time we get Ben-Polly-Two, it's Ben-Polly-Jamie-Two. Only a couple of Dodo stories exist too. Likewise, the only completely intact Jamie-Victoria-Two series is set on a very cold planet. (It appears that Victoria updated her wardrobe after her first appearances.) Zoe's episodes mostly survive despite her looking sexy partly because her skin is completely covered by catsuit and partly because VCR tech was starting to trickle down into more homes.


 * A fair bit of footage from that era only exists today specifically because it was retained in censorsâ€™ archives.
 * That only josses details. The censors might go easier than the Arabs on sexual imagery, but they'd likely object to much of the same stuff. When the era of free love ended, it crashed.
 * Unlikely. You'd think there'd be more accounts of it, or modern 50+ people telling tales of wanking to the episodes, or their memories of them.

The Doctor never got over his possession by Sutekh in "The Pyramids of Mars"
Self-explanatory. Sutekh turned the Doctor into his puppet, and the Doctor only thought he got free. He has been carrying out Sutekh's will by destroying everything.

The Time Lords are descended from Sidereals.
Bureaucratic, arrogant, scheming, double dealing, watching the universe from isolation while using others as their agents (in a very hush-hush-no-we-didn't way) to control the universe, able to warp time on a personal level, and capable of mental communication and ESP, whose only proactive members have to go into exile. Death is even one of their gods (according to the spin-off novels).

Zoe comes from our time.
She knows of the Karkus, a cartoon character from the year 2000. 2000 has already passed. Therefore, it's entirely possible that she's from what is now the present day. It's known that the Doctor Who universe has more advanced science than ours, especially in and beyond the 21st century; creating the Wheel in Space should be no problem, since they've managed to send astronauts to Mars already.
 * She was "born in the 21st century," so she can't be from any earlier than 2015 or so. But that's now close enough to be Twenty Minutes Into the Future.

The Doctor is not only the Valeyard, but also the Master!
Given how power-mad the Seventh Doctor became with his act-of-god actions, and given how war-crazed Nine got, it's clear that Time Lords just get crazier and more megalomaniacal as time goes on. (Does Yen look well-adjusted to you?) So he becomes the Valeyard, and then The Master, and then he goes back and inserts himself in his own timeline and attends the Academy with himself. Then in a fit of madness, he starts the whole mess that causes The Doctor to flee Gallifrey with his granddaughter in the first place.

The Sixth Doctor was not 'totally tasteless' as many people claim.
He simply wore the outfit to piss off as many people as humanly (...Gallifreyanly?) possible.

The Doctor is The Doctor mkII - or, in modern parlance, the Doctor 2.0.
Recently suggested by the Doctor Who Magazine. Like the Master, the Doctor was revived by the Time Lords. This would explain why, in the "Brain Of Morbius," he was in his fourth body and why we saw faces before that. They were of the Doctor mkI.

The First Doctor had a heart attack from which he never recovered.
Since he had a heart in reserve, it wasn't life-threatening enough to cause regeneration. He just went on with only one WORKING heart; the other repaired itself when the next regeneration came along.
 * The problem with this theory is that the Doctor was never treated as having two hearts until the Third Doctor.
 * It was so bad that it took TWO regenerations to fix?

The Flip-Flop two-disc audio set was a connecting point between two different parallel dimensions.
Doctor B caused  and Doctor W. Not the same guy.

The Karkus comes from a webcomic from the year 2000.
Well, you haven't seen him in your newspapers, have you?
 * Unfortunately, that webcomic was hosted on Geocities.

The Fifth Doctor is a rampant sociopath trying to work for the forces of good.
Let's examine this one, ok? He decides the only way to deal with a mostly-harmless obese frog-alien is to splash him with a deadly poison. He's a serial killer, albeit not convicted. The Fifth Doctor has repeatedly shot a dying alien in the chest because he could. He nearly let the 'villain' Omega blow up the universe before deciding to shoot the guy anyway. Then he decided to end a war between humans and aliens by killing every single person there for the sheer hell of it. To stop the Master, the Doctor chose to wipe out the population of an entire world. In a later encounter, the Doctor banished the Master to the distant stars alongside an alien race who would be wanting to kill the Master for his deeds that adventure. And when it came to a multi-Doctor adventure, he's the only one to be seduced by evil.

Perhaps finally, the Fifth also sat by and watched as his archenemy burned to death with a look of Dull Surprise on his face... in an adventure where he already killed a companion with his own hands and decided the best way to heal the mortally injured was to set them on fire.

Oh, and he was directly involved with starting the Great Fire of London. Not only did he start it, but he openly built up the fire and made it larger than it would have been.

Come on. The Fifth is a rampant sociopath, but it seems to only be obvious in retrospect. And even then, most of the survivors forgive him because he did mean well and because he's cute.


 * Is that why the Tenth Doctor is such a fan of him?
 * Well, considering that the Tenth straddles a line between Chaotic Good and Well-Meaning-Sociopath every day, very likely. Ten likes Five for being young and liberated, the first to be free of the strictures of his earlier selves - and since "his earlier selves" includes the free-spirited bohemian Four, Ten must be thinking of this rampant but well-meaning sociopathy.
 * In the novelization of The Twin Dilemma, the Doctor comments that, as Five, he was "on the verge of becoming neurotic". We might not have understood at the time because Six had his own mental issues around then, but now that we've had time to think about it...
 * To further expand, one can even see this explaining why the Fifth was so damned energetic at times... sure, he just killed off god-knows-how-many people averting this adventure's disaster, but at least he saved so many others through his actions - or tried to save them, at least. In fact, Nine and Ten are kinda like this - Tenth even more than Five. Although Nine and Ten at least show remorse before someone points out what they did... which also makes Five seem like a little like a child given a loaded gun and not understanding why the loud noise made their dog die. Again, lending credence to the theory.
 * So, Tegan was the primary force keeping Five from losing touch with reality completely?
 * Honestly, this troper (and creator of this WMG) would not be shocked one bit. Right after Tegan leaves, the Doctor randomly curses at the not-present Daleks for several minutes before Turlough dares to speak up, and he certainly seemed to be losing it a little bit during his time with just Nyssa (anyone else think he accepted death just a little too easily?). It certainly seems like Tegan was some sort of a stabilizing force in the Doctor's persona - though Peri seems to have been a stabilizing force as well, seeing how the Fifth didn't randomly leap into insanity during his final story. One can only wonder what would have happened had Tegan not returned to the TARDIS...

Davros is Stephen Hawking
Crippled and in a wheelchair? Check. Brilliant scientist? Check. Large ego? Check. Survived something they shouldn't have? Check.

Sometime in his youth, Stephen Hawking was made immortal in a similar manner to Jack Harkness. This is how he is still alive when he was projected to be dead within two years of being diagnosed with motor neuron disease. Eventually, he ends up on Skaro several millenia in the past. Kaled medicine restores his ability to speak and turns him into one of them, driving him insane in the process. The Dalek voice is based on his own speech synthesizer voice.

To prove this theory, someone must get Stephen Hawking to do a Dalek imitation.

Time Lords only have titles, not names
Though some of those titles are pretty obscure. (What's a Borusa, anyway?)

Time Lord names are granted only after they become Time Lords
Before, they use whatever name they were born with or are used to. They enter the Academy, go through hell, and emerge as a Time Lord; then they are given a new name that suits their personality, and they embrace this new identity and never look back.

The link from Old Who to New Who is not direct -- it goes through a severe Temporal Paradox
So, according to New Who Word of God, nothing is explicitly non-canonical. That means the Faction Paradox novels are true. And that means that one of the Eighth Doctor's former companions killed the Third Doctor about one series arc too early.

Problem: The last serial of the Third Doctor's almost certainly cannot be solved without someone dying. It cannot be prevented, either -- the Doctor gave that jewel to Jo Grant some time before; if he wants Sarah Jane to live, odds are he'll have to die. And Four loved Sarah Jane as much as he loved any human...

So, from getting Four early, we are forced to get someone like old-series Five early. This is why Sarah Jane was able to fall hopelessly in love with the Doctor. We'll get at least parallel Sarah Jane episodes and parallel Romana episodes (including E-Space -- and yes, Five + Key of Time is a scary thought).

This Five will not die by radio tower. He'll be hurt, perhaps severely, but he won't regenerate. He may refuse to (he managed to delay regeneration on Androzani for some time the first time around). So we'll get variants of the normal Five episodes, likely up to and including the Androzani disaster.

If the Time War hadn't already been violently settled when Five had the Key Of Time, then the Time War will gain heat about when "Trial of a Time Lord" happened in the original timeline. Six will cast the killing blow here like he did to Skaro -- or else Nine will. The Doctor will remember Seven and Eight -- he's a Time Lord and knows how things might have gone -- but this time around he'll never have been them. Nine got a few of the Seven genes; Eleven might get a few of the Eight genes.
 * Excellent theory - but this troper is a little more worried about how Genesis of the Daleks would have unfolded than Key to Time... though that's possibly due to the fact that he's yet to see the Key to Time arc. Either way, a longer tenure for Five also means a much higher death count throughout the stories thanks to how his own stories happened...
 * "Genesis of the Daleks" couldn't get much more bloody than it already is and still allow for NuWho canon (we still have Daleks, after all). Maybe Harry dies.
 * Remember how powerful the Time Vortex is? The Key of Time has the same power to change space-time, only it doesn't kill the Time Lord incarnation who's using it. (Probably.... though, given that Romana regenerated at the beginning of the next season...)
 * And a higher death count would help explain how the Doctor of New Who sees himself ("The Oncoming Storm") and how surviving higher lifeforms see him. Four did get caught in a few genocides (he once reprogrammed a computer because he felt like it -- and did it wrong), but Five has triggered at least two simply because he showed up.
 * Also, perhaps the Fifth Doctor would have been much more jaded by the time of his 'original' stories in this new continuity. After all, 7 more years of death and destruction around him could not be good for the psyche - even for one as well-adjusted as the Fifth's tended to be. Maybe he'd be (gasp!) Genre Savvy enough to notice when the Master showed up.
 * One more side effect of this theory -- maybe the NuWho Doctor isn't lying about his age -- not strictly, anyhow. In classic continuity, the Doctor was 941 when he shifted from Six to Seven, and it is presumed that he was Six when he was 900. In the paradox iteration, whatever caused the Doctor to turn into Nine could've happened right when, or shortly before, he turned 900.
 * The Third Doctor-died-early paradox was settled in the novels themselves:
 * Okay, general theory confirmed, details jossed? (Ontological inertia being what it is, defeating Grandfather Paradox probably shouldn't bring Three back -- but, since the Timey-Wimey Ball rules Doctor Who time travel...)

The Rani is Holly Marshall.
In the 1974 Land of the Lost episode "Elsewhen", Holly encounters a blonde woman, apparently in her twenties, who calls herself "Rani", who turns out to be Holly's older self come back in time to help her. Rani admits that she can time travel at will and understands the technology of the Land. Given that the pylons of the Land display TARDIS-like properties, it seems plausible that at least one is a TARDIS; the future Holly used it to escape the Land to Gallifrey where she became a Time Lady (just as Ace would have if the classic series had never been cancelled).

Adric has Aspergers
He's socially awkward, he doesn't seem to realise when he's offended people, he tends to take things too literally, and, of course, he loves maths and logic.
 * This troper has Asperger's and he hates math.

Adric's entire species is short on empathy deep down
We see his people and learn the secret of his species in his first serial. Only one form of his species looks fully humanoid; the other two are closer to arthropod. So Adric probably is more like a super-intelligent spider, mentally, than like a normal human being.

In "Terror of the Autons," the Third Doctor didn't say "Tea-Lady"; he said "T.Lady"
"This place is strctly out-of-bounds to everyone but the Brigadier's personal staff and the T.Lady."

As in abbreviation of Time-Lady who is his probation officer - except he's under sentence rather than on probation. The Doctor isn't exactly forthcoming about being a convict; he just says that the secret of the TARDIS has been taken from him, probably so as not to affect his career in a military organisation. So when a member of his own species turns up every now and then, he says just that, rather then her occupation.

The Third Doctor has a prisoner tattoo
We see a glimpse of it in his debut serial. After that, he always wears long sleeves. The tattoo is meant to warn other Time Lords not to let him hitch a ride on their TARDISes. He still bore it after "The Three Doctors," but the Time Lords did rig it so that when he regenerated again, it wouldn't stick.

The Eighth Doctor partially foretold the events of Journey's End in the TV Movie
The Hand Doctor is half-human. His human side comes from Donna, making her his mother. As the Eighth Doctor was very prone to prognostication, this is what he was actually talking about.
 * Possibly Jossed by the comic mini-series Doctor Who: The Forgotten. It is revealed in a flashback involving The Eighth Doctor that The Doctor's claims to be half-human, as well as his erratic behavior during the TV Movie, were all part of a Xanatos Gambit to throw The Master off-guard, accomplished in part through a half-broken Chameleon Arch (a.k.a. The Eighth Doctor's trademark fob watch!)
 * Well, you picks your Expanded Universe Alternate Continuity and you takes your choice. The BBC Books Eighth Doctor Adventures had already explained that the reason the Doctor said he was half-human was ... that he was half-human, son of a Time Lord called Ulysses and a human called Penelope. (Penelope Gate from the Virgin novels? Could be...)

Ian and Barbara were killed in The Stolen Earth/Journey's End
As soon as they saw a Dalek, they would have known the Earth was in deep shit. What they couldn't have known is that this is a different faction for whom the mud-on-the-lens trick doesn't work. They were probably awesome to the last, and likely died bravely.
 * As depressing as this is, I put this in my own personal Canon. Along with the WMG of the Dr. Who movies being anti-Dalek warning movies, this just makes too sense to not be true. Ian and Barbara, you shall be missed.
 * Jossed in Sarah Jane Adventures "Death of the Doctor".

The Master in some of the spin-offs isn't really the Master
David McIntee once had a throwaway idea that, when the Master was being cured of his Cheetah Virus in his novel First Frontier, a clone was created, and this was the Master in the TV Movie. While he never actually used this theory in any way (except in attributing a quote from the TVM to "the (ersatz) Master" in The Dark Path), it's a fun idea. Looking through the spin-offs there appear to be two clones, plus the Master. The timelines go like this.
 * The Real Master: First Frontier -> Happy Endings -> The Adventuress of Henrietta Street (as the Man with the Rosette) -> New series.
 * Note that the Man with the Rosette says that he is clean shaven because the Doctor has a beard. Therefore the last time he met the Doctor they can't have both been clean shaven, therefore he isn't the TVM Master.
 * Clone #1: First Frontier -> Dust Breeding -> Master
 * Big Finish audios version, who reverts to the Geoffrey Beevers incarnation.
 * Clone #2: First Frontier -> The Eight Doctors -> The TV Movie -> Sometime Never... -> The Gallifrey Chronicles -> The Glorious Dead (Doctor Who Magazine strip).
 * This is the version who got trapped in the Eye of Harmony and spent a couple of novels appearing on a screen in the TARDIS. In an alternate timeline where the Doctor regenerated into Richard E. Grant, his conciousness was transferred into a robot body that couldn't leave the TARDIS (Scream of the Shalka).

Melanie, known as 'Mel,' was a companion of the Seventh Doctor first.
Ok, bear with me on this one. During the third part of Trial of a Time Lord, we are randomly introduced to the new companion Mel. In fact, the Doctor points out that this doesn't take place long after the conclusion of the trial... but we never saw when the Doctor first met Mel. In fact, the series skirts around this by instead having the first televised adventure of Sixth and Mel together outside the trial run right into the Seventh Doctor's regeneration. The key problem here?

Unlike practically every other companion to be there for a regeneration, Mel doesn't bat an eye at this.

So, considering the time-traveling apsect of Doctor Who, this could mean that Mel first met the Seventh Doctor rather than the Sixth. This helps explain why we never see Mel officially join the Sixth Doctor, and helps explain why the Sixth Doctor just wanders off with her at the end of the Trial without the Time Lords objecting.

In terms of how this fits the timeline, it must be further along the Seventh Doctor's lifespan after the show was placed on hiatus. The Seventh Doctor, being incredibly clever at this sort of thing, realizes that this is before the Master snatches Mel randomly from time and space and gives her a small explanation about some key things before she's dragged back in time later on. Odds are also good that many of the Seventh-and-Mel audio dramas and novels can take place in this time unless specified - especially considering there wasn't a whole lot of offscreen time given to Mel and Seventh. Of course, Mel is eventually ripped from her time with the Seventh and sent to help testify his case, and time unfolds as we've already seen before.

...ok, so it's a little convoluted to explain away why Mel doesn't seem all that disturbed at the Doctor regenerating, ; but with this franchise, pretty much anything goes.

The Meddling Monk worked with Cessair of Diplos for a time.

 * She commanded the Stone Circles, and he helped with Stonehenge...

The Brigadier, Jo, Tegan, Ace, and Grace all recognized Mr. Saxon for who he was.
Of course, there was little that Tegan or Grace could do, being citizens of other countries. And Jo was in the Amazon rainforest, so she probably didn't vote in that election, either.

The Rani has never appeared in the new series because she's too busy being Rani Mukherji
Thoda Pyaar Thoda Magic, Dil Bole Hadippa and Saawariya all contain clues as to her true identity. In TPTM she is a nearly immortal being. In Dil Bole Hadippa she spends much of the movie in disguise, hinting that Rani Mukherji is not as she seems. And in Saawariya she plays a character that's narrating (from afar!) a story that may or may not be true; sounds pretty Time Lord, right?
 * None of these movies did well financially, meaning few people are picking up on these hints; eventually, she'll go crazy in 2012 and cause the end of the world.

Sozin and Roku were previous regenerations of The Doctor and the Master
Right down to the frolicking in fields and the gay and the mutual adversarial respect.

Every Doctor we have seen is official
We all know that as well as the Doctor that we know and love there have been others such as The Shalka Doctor, The Curse of Fatal Death Doctors, Dr. Who and (Evil) Future Doctors; such as Merlin, Muldwych and the Valeyard. This is how they all fit into the Doctor's personal time line.

The Curse of Fatal Death Doctors: Rowan Atkinson's Doctor was the true Eighth Doctor, chronologically speaking. After rapid regenerations, the Doctor eventually becomes a woman. It is during this female incarnation that The Last Great Time War starts.

When she returns to Gallifrey, The Doctor has some of her regenerations restored and becomes someone who looks an awful lot like Seven, and then the person we call Eight.

Now for the interesting part. During the heat of the War, the TARDIS saved the Doctor from Gallifrey, forcibly removing him from the battle and refusing to return to Gallifrey.

Angry at the TARDIS, the Doctor ejects the Eye of Harmony (possibly trying to kill it) and ends the war.

Distraught and alone, the Doctor returns to the one planet he was ever able to call home besides Gallifrey - Earth. He uses the chameleon arch and becomes the human we know as Dr. Who. This human Doctor holds inside of him some memories of his past life, such as Susan, Skaro, the Daleks, and the phrase TARDIS.

This explains why Tardis (Doctor Who's ship) is a police box. This Doctor is constantly going back to the Daleks (that is, to places he has been before) to try and stop himself from starting the War in the first place.

At the end of these adventures, Doctor Who finds his Fob Watch and becomes The Doctor once again - specifically, the one we call the Eighth Doctor, but physically older. (It was a long war.)

The Doctor offered to take his family travelling with him. They rejected the offer, feeling that the man they knew was a lie, and they would hate the Doctor. Either that, or they do come with him and live out their lives in the TARDIS.

Either way, human lifespans being what they are, the Doctor winds up alone again. So he hits random on the TARDIS and ends up stranded on Earth for 100 years, thus becoming Muldwych. (He chose to call himself Muldwych because he knew he would tell his past self that this was his name.) These hundred years were in the time of King Arthur, explaining why he also took the name Merlin.

Over time, he would return to his TARDIS and drift through space for many years/eons and end up looking like the Shalka Doctor. It is in this form that the Eighth Doctor dies...simply from getting old. He dies and regenerates into the Ninth Doctor (Christopher Eccelston).

As for the Valeyard, he is either, as he claims, a later incarnation of the Doctor who found himself back on Gallifrey (probably driven insane by breaking the Time Lock ala Dalek Caan)....

Or the Meta-Crisis Tenth Doctor (aka Ten(b)) as many people think (possibly including the original Ten.) This Half Human Doctor wanted to frame his other self to get regenerations, as he had none in the first place.

Ace founded the Time Agency.
The New Adventures used to be canon and are still deuterocanon; it's possible that many events in the books happened. Ace may have been last seen as a time-travelling vigilante with a wrist-mounted computer and a firm belief in peace through superior firepower. What's the Time Agency but a bunch of time-travelling vigilantes with wrist-mounted computers and no real aversion to the use of superior firepower to bring about peace? And the fall of Gallifrey ensured that Ace would pass her vision on.
 * Russell has said that "canon" isn't something he worries about; he's quite happy for the fans to decide what they consider canon. He even offered an explanation for how Gallifrey has apparently been destroyed twice, suggesting that at some point it was resurrected, only to become involved in the Time War with the Daleks. (The books and audios have taken this comment and run with it.)
 * It would be totally awesome if it turned out Ace founded the Time Agency.
 * And this could be why Jack lost two years worth of memories. At some point he was helping the boss on a two-year mission and Ace was reunited with the Doctor towards the end of it. He told her about the vital role Jack would play in his life, and to ensure that came to pass she wiped her top agent's memory, creating a classic Stable Time Loop.

The Black Guardian is the same being as the Trickster in The Sarah Jane Adventures.
Let's examine this: uber-powerful being dressed all in black who hangs around just outside reality, making Faustian deals with people? And gives them little trinkets to remember him by, backed up with gentle verbal persuasion if necessary? And says "Waking or sleeping, I will be with you always"? C'mon!

Rani Chandra is The Rani
There is no way both characters have the same name and do not have a connection. By the way adding this to the "Luke Smith is the Doctor" theory above, it would mean Clyde Langer is The Master.

Doctor Who is a TV Show within its own canon.
Don't ask me how The BBC managed to get a hold of this info.
 * It is; Eastenders exists within Doctor Who, and Doctor Who exists within Eastenders, ergo DW must be a TV show within DW.

The events of Curse of the Fatal Death were all just a weird dream had by the Eighth Doctor.
This might explain his initial shock and surprise at

Whatever caused Romana to regenerate was the same thing that gave K-9 laryngitis.
We just didn't see it happen.

The Sixth Doctor was a Tsundere.
After attempting to kill Peri during his regenerative crisis, he felt extremely guilty but was too shy to admit it. He used his arrogance as a cover-up. If we had seen any of his adventures with Mel, then he would've softened up a little.
 * Supported by his Big Finish audio adventures.

The Meddling Monk hears drums.
The Master did not always go by "the Master". Up until Terror of the Autons, the Doctor had him written off as a jackanapes. The Master also has a vendetta against the Doctor. Hmm...

The Vogans restore and reuse alien rockets.
That explains why that rocket has "United States" on it.'

Jo Grant shot the Master in "Frontier in Space."
At the end of "Frontier in Space", the Doctor is shot at by the Master and falls down unconscious while Ogrons run about and general chaos reigns. There's a sudden cut, and we see Jo hovering over the Doctor, with no sign of any Ogrons or the Master. And Jo, for some reason, has the Master's weapon in her hand. While the Doctor was unconscious, Jo, believing him to be dead, wrested the gun from the Master and shot him, forcing him to retreat to his TARDIS and escape; this explains why he did not remain and prevent Jo and the Doctor from escaping. The Master was on his final incarnation, and so either tried and failed to regenerate or prevented himself from regenerating, and this caused his body to decay into the husk we see in "The Deadly Assassin" and "The Keeper of Traken".

Marinus orbits a red dwarf star.
It is pretty clearly a human colony (noone corrects the Doctor when he refers to them as human, and there are wolves hanging around), and yet Arbitan is over 2000 years old, and Yartek not much younger. Obviously, we are talking about very short years.

Salamander was a good man when he invented the Sun Store.
Afterwards, he was granted power and it went to his head.

Eventually, Ian and Barbara deduced the truth about how their old boss really died.
They wouldn't know about the different Dalek factions until the Medusa Cascade, however.

Edward Waterfield was given descriptions of all thirteen Doctors, and all known companions.
How were the Daleks to know, until they got the security photo, which Doctor and companion(s) they would be dealing with? There were two different Doctors in this time frame alone, after all.

Trantis from "The Dalek's Master Plan" is a Dominator.
In "The Daleks' Master Plan", delegates from all the outer galaxies form an alliance to attack and conquer the solar system. This is reminisced upon in "The Dominators", when the henchman Tober mentions that the Dominators are "masters of the ten galaxies". This sounds rather implausible, but upon simple observation, one can see that Trantis bears the most resemblance to the Dominator species, among the outlandish variety of aliens that form the rest of the council. The simple explanation is that the Dominators from Trantis's galaxy, while fairly powerful in their own right, have a serious case of power delusions, and see themselves as masters of the universe. This goes unmentioned in the Master Plan (most likely to avoid pissing the Daleks off), but is evident in The Dominators.

The Weeping Angels are derived from the Medusa statue seen in "The Mind Robber".
Said statue appears as stone but comes to life as the heroes look away, has a very strong physical resemblance to the Angels, and it's dangerous to look into its eyes, which is also how the Doctor defeats it: forcing it to look at itself. Thanks to the Timey-Wimey Ball, a race of interspatial killers was born from that very statue (or alternatively, the historical Medusa) and went on to torment the newer Doctors.

The Fifth Doctor's celery was more than just a decorative vegetable.
This explains it all.

One (or both) sides in the Time War arranged the assassination of the Seventh Doctor.
So, the Seventh Doctor... kind of gets killed for no reason in the Made for TV Movie. Or does he?!

The Seventh Doctor, as we all know, fancies himself The Chessmaster, and he's certainly the kind of Manipulative Bastard who'd have all kinds of plans and schemes for dealing with the Time War and the various problems arising from such an eventuality, both Dalek and Time Lord (particularly those keen on a bit of Ultimate Sanction and ascending to Godhood) related. And he's pretty good at them as well, which means he's exactly the kind of dangerous threat that has to be dealt with or at least neutralized. The Eighth Doctor, however, is a bit flighty, not really the sort for planning ahead, a bit sensitive and sweet -- not really the sort who's equipped to fight a horrific intergalactic temporal war. Quite a coincidence, then, considering he's the one (apparently) who ended up fighting it. Almost as if someone planned it that way.

Here's how it goes; whoever's behind it first makes a deal with the Master. You're dying, pretty much on your last legs anyway -- get yourself 'killed', demand that the Doctor bring your remains back to Gallifrey personally, and then distract him and divert him somewhere where he's likely to be killed (or at least regenerate). Say, a dark alley in a dangerous, crime-ridden part of town in San Francisco. To sweeten the deal, you can have his remaining regenerations. The Master agrees, allows himself to be turned into that snake-goo thing, and the Doctor comes a-calling. The Master gets into the TARDIS' inner-workings and buggers around a bit, sending him to Earth (and, incidentally, knackering up the external scanner, meaning the Doctor can't see what's outside even if he doesn't just charge out the door like we've seen him do so many times before -- which also explains that whole "why doesn't the Doctor just check the scanner" plothole everyone complains about as well). That's Part A; get the Doctor to Earth.

Part B concerns those gangsters who try to kill Chang Lee. At least, that's apparently why they're there,and certainly why we assume they were there -- they certainly shoot his mates, but when Chang Lee's dead in their sights, they just sort of stand there and sneer for a bit. As if they're waiting for something else. They've obviously been lurking there a while, given that they were hiding when their supposed 'targets' were just happily walking away, and only revealed themselves after their presence was accidentally exposed. Then the TARDIS appears -- not only right in front of Chang Lee, but conveniently exactly where the gangsters have a perfect shot at whoever happens to walk out the door. They shoot it -- and then reload, wait for the Doctor to come out, and then shoot him. And then bugger off, without even bothering with Chang Lee -- who, we're led to believe, they're supposedly there to kill in the first place. They were never interested in Chang Lee really -- they were hired by parties unknown to whack the Doctor, and Chang Lee and his mates just stumbled upon them (probably on the run from those gangsters who were after them) and had to be silenced as witnesses. Of course, they've probably got no idea why they were hired or what they've been part off -- they are notably freaked out by the TARDIS -- but it's either a hell of a coincidence or someone's arranged things so that the Doctor appear in that exact alley at that exact time when a whole load of machine-gun packing gangsters just happened to be spraying bullets around. If he gets shot and dies there and then, great -- if not, he gets carted off to a human hospital where, having no understanding of Time Lord physiology, they'd no doubt bugger up somehow and probably end up killing him anyway. Either way, result. And whether the Master (who the Time Lords, as we eventually learn, are quite happy to use as a puppet) gets a new body or, as even the plotters would have to concede is more likely, the Doctor gets a new regeneration, either way The Chessmaster that is the Seventh Doctor is taken out of play. Win-win.

So who's behind it? Obvious money's on the Daleks -- they've got an obvious motive, what with the whole 'arch-enemy of the Doctor' thing, and it would explain why they suddenly developed that interest in legal niceties and put the Master on trial rather than just exterminating him first and not even bothering with a question. But given the complex nature of the plot described, the Time Lords -- who love these kind of byzantine plots and scheming, aren't exactly immune from being bastards to the Doctor even pre-Time War and have that whole Ultimate Sanction plan in a drawer ready to be pulled out whenever they feel like becoming Gods (and they have to know the Doctor ain't gonna like that) -- are suspects as well. Plus, a new Doctor might be more malleable and easy to handle than the Seventh Doctor, who has his own plots and schemes on the boil as well.

Either way, the Seventh Doctor did not die randomly. He got put into checkmate.

Ian and Barbara knew about regeneration.
In part six of The Keys of Marinus, the Doctor would have had to consider the possibility that Susan might be killed and regenerate. He would have had to warn Barbara, Sabetha, and Altos that Susan might look quite different.
 * Thete didn't know about Susan's kidnapping.

Tavius was the first to use the cross as a symbol of the Faith.
The purpose of the pendant was to symbolize the command to take up one's cross daily.

Zoë negated her own timeline in The Invasion.
One problem that crops now and again in Doctor Who fandom is what order the Second Doctor's three "21st-century" stories (The Moonbase, The Wheel in Space and The Seeds of Death) are supposed to take place in. You end up with a contradiction whichever order you choose: So they all come before each other.
 * Wheel comes before Moonbase, because in Moonbase everyone knows about Cybermen but in Wheel no-one does.
 * Moonbase comes before Seeds, because the weather control's less sophisticated and the plot wouldn't work if T-Mat had been around at the time of Moonbase.
 * And Seeds comes before Wheel, because in Seeds humanity never got beyond lunar orbit but in Wheel they're out as far as the Asteroid Belt. But Wheel comes before Seeds because Zoë isn't familiar with T-Mat (or Ice Warriors).

Here's one solution: By travelling into her own past in The Invasion, Zoë changed the timeline. In the original timeline, Vaughn's plan worked; he gained control of the Cybermen, became dictator of Earth, and used their technology to get humanity spread all over the inner Solar System. When Zoë shot the Cybermen's fleet out of the sky, she negated that entire timeline and humanity never got further than the Moon.

Arcturus told Hepesh about the Ood.
Peladon and Torbis, meanwhile, thought the whole thing was propaganda.

The Sixth Doctor's instability was a backup plan of the Master's that didn't work properly
As the Fifth Doctor lay dying, he hallucinated his incarnation's companions urging him to stay alive, something similar to what he saw as the Fourth Doctor was dying. However, he suddenly hallucinated the face and voice of the Master ordering him to die and laughing evilly, almost drowning out his friend's voices. He'd a few moments before mentioned how the regeneration he was starting to go through felt different than before, and the Sixth Doctor was clearly unbalanced and barely holding himself together. So, what happened? When the Fifth Doctor was recovering in Castrovalva, which turned out to be a trap of the Master's, the Master took the oppertunity to plant a cruel psionic suggestion in the mind of the vulnerable and recovering Doctor as a backup plan in case the Doctor once again escaped his clutches, designed to kick in when he regenerated next to try and make the Doctor unconciously abort the regeneration. Much later, in The Kings Demons, when the Doctor failes to psychically take control of Kamelion from the Master, the Master mocks him by calling the Doctor weak minded...and then suggests that it's time for the Doctor to regenerate, a comment that doesn't make any real sense. This was a veiled reference to the suggestion that was planted in the Doctor's mind. When the Doctor did eventually regenerate, the suggestion kicked in, which was the hallucination of the Master. The companion hallucinations were the Doctor's mental defences fighting the suggestion. The result was that the Doctor overpowered the suggestion and survived the regeneration...but severely damaged his sanity doing it. Over time, with Peri's help, the Sixth Doctor worked to recover his sanity...until Sil re-opened the mental wound in Mindwarp, ruining the Doctor's recovery and leading to his insane behaviour prior to his trial. Maybe it was even this mental damage that caused the beginning of what might one day become the Valeyard?

Grace and Chang Lee are immortal like Jack
They were brought back to life by the TARDIS.

By the 51st century, Desperus was civilized
This troper came away from Planet of the Ood with the sense that worlds like Desperus were where the Harriet Beecher Stowes and William Wilberforces of the 2G&BHE tended to wind up.

Steven Taylor used the Zero Room
He was none too stable, except when Vicki and the Doctor hear him in the TARDIS, he's calmed down quite a bit. The Zero Room's calming influence did the trick.

Silurians are somehow related to the Ice Warriors
I haven't seen any of the classic Silurians (only Smith era), but those silurians look rather similar to the Ice Warriors as seen on Peladon. They certainly look alike, they have the same green skin/scales. And they both wear head coverings and green clothes

Six looked like Maxil because...
Romana looked like Princess Astra because she liked her appearance, so the Doctor took Maxil's appearance because he liked it.

The Seventh Doctor is Ace's biological father
Not sure if this is canon due to not having seen enough Ace episodes, but I don't think we ever learn the identity of Ace's father, and they are eerily similar...

Susan's parents were killed by The Master
A little theory I came up with. The Master killed Susan's parents out of hatred for the Doctor. Thats why he left Gallifrey to escape the guilt of his child's death. he took Susan to protect her from the Master. Then to stop her sadness he Chameleon arched her to erase her parents out of her memory but having them be in the back of her mind (Hence her calling One Grandfather). But around Dalek Invasion of Earth she started to regain those memories. The Doctor out of fear of her anger and her sadness he left her on earth claiming it to be for her to grow up (hiding the real reason of protection for the both of them). In my version Sam Beckett tells Five to go to her and reconcile.
 * Thete had the Master written off as a jackanapes before Terror of the Autons.

If the TARDIS had arrived in Spain at that time instead of Tenochtitlan, Barbara would have tried to ensure that Castile did not come out on top.
Castile, which took over most of the peninsula, was the really nasty Proud Warrior Race. And while the conquistadores had to keep Queen Isabella deceived about what they were doing lest they be hanged, that was only while she lived; the Castilian ethos made the US Indian Wars look tame. And Barbara's goal was to avert the Evil Versus Evil aspect of the Spanish vs. the Aztecs.

That woman who griped at Seven right after the climax of "Survival" was Jackie Tyler.
The one who shows up here at the 1:55 mark. She's just credited as "Neighbour"...
 * "Survival" took place in Perivale around 1989, while "Father's Day" indicates that Jackie moved to the Powell Estate in Peckham some time after 1987. Not too difficult to reconcile, one way or another.

Romana didn’t waste ANY regenerations in “Destiny of the Daleks”
We already know from the new series that the regenerative process lasts a while and grants extraordinary healing powers during that time. We also know from “The War Games” that if the regeneration occurs when a Time Lord is NOT on the brink of death, they can choose their new appearance. With those things in mind, since Romana actively chose to regenerate, all those different forms she tested were before the regeneration energy dissipated and stabilized her into the copy of Princess Astra she wanted in the first place. Sort of like forming a sculpture out of wet cement in that you can make it into any shape you want before it sets, it’s just permanent afterward.

When the Eighth Doctor said he was half human, he was talking about 10b.
The Eighth Doctor claimed to be half human on his mum's side. Given that Donna is the one to touch Ten's hand, it ould be argued that she is 10b's mother. And given that fact that she's human... THE DOCTOR IS HALF HUMAN!
 * He was talking about someone who he doesn't know even exists. Due to the wibbly wobbly nature of the Time War, maybe he doesn't at all then.

Susan's grandmother is The Master.
I'm surprised this isn't already here (And yes, I did check.) We know from the New Series episode "The Doctor's Wife" that time lords can change gender, and it's nowhere near a stretch that The Doctor loved The Master that way before he turned evil. The Master was a woman in one of his/her regenerations, and she and the First Doctor had one or more children. One the children was Susan's mother or father.