Theory:Doctor Who television discontinuity and plot holes/The Ultimate Foe


 * At the end, The Doctor acts as if he's sick of exercise and carrot juice. But from his standpoint, he hasn't exercised or had any carrot juice.  That's in his future.  Mel saying "we'll get you back on the exerciser" makes sense, because the scenes of the Doctor exercising are in her past.   But the Doctor hasn't lived through all that.  He only watched it briefly.  So he wouldn't be sick and tired of exercising and carrot juice.  "Carrot Juice, Carrot Juice, Carrot Juice".
 * Perhaps the Doctor hates carrot juice and exercise so much that just thinking about it makes him sick and tired.
 * He's not acting sick of it, he's acting petulantly about it. He simply doesn't want to drink a whole load of carrot juice and start exercising, especially not immediately after he's just come off being put on trial for his life and forced to battle an evil possible future version of himself.


 * Mel leaves with the Doctor at the end of this story, despite being from the Doctor's future.
 * This is extremely odd, since it dramatically increases the probability that this "older" Mel will encounter her younger self at some point, and fall victim to the Blinovitch Limitation Effect. This possibility was neatly sidestepped by the following story, Time and the Rani. Since it immediately depicts the regeneration of the Sixth Doctor, there is presumably a wide gap between it and Foe. The arrival of the Seventh Doctor instantly mooted any televised treatment of the asynchronicity between the Sixth Doctor and Mel. Nevertheless, the issue has been addressed in other media. In the novelisation there is an epilogue in which the Doctor returns Mel to his own future self, who then embarks on the journey that leads to Lakertya. This assumption was followed in the PROSE: Time of Your Life, where writer Steve Lyons posited that the younger Sixth Doctor immediately took Mel back to his older self. The issue of the Doctor's knowledge of Mel prior to their first meeting is examined in PROSE: Business Unusual, while the fact of there being a substantial interval between this story and Time and the Rani has been addressed through the myriad of novels and audio dramas featuring the Sixth Doctor, yet taking place between the trial and his official first meeting with Mel. An alternative assumption is made by The Universal Databank which speculates that the events of the Trial destroyed the future timeline Mel was from.


 * Or maybe, despite the conclusion offered in The Ultimate Foe, it's just a paradox (hardly unknown in Doctor Who) and neither Mel nor the Doctor actually remember how they first met because there never was a first meeting (it's wibbly wobbly, timey-wimey, as in Blink) - especially as the Doctor won't remember events from his future witnessed at the trial (remember the War Doctor's words at the end of The Day of the Doctor) and the inability of "earlier" Doctors to recall their encounters with "later" Doctors (as in The Three Doctors, The Five Doctors, The Two Doctors, and Time Crash.


 * Actually, Time Crash clearly shows that this is not a universal rule, and the Doctor does remember some multi-Doctor stories. It's wibbly-wobbly like everything else.


 * Also, AUDIO: The Wrong Doctors explains this, but the way in which it explains it can't really explained without a) this being way too long and b) me revealing spoilers for that audio if you haven't listened to it yet because the way in which it does so is the entire plot. But, most basically the sequence goes;


 * For Mel:


 * Mel meets Doctor (PROSE: Business Unusual) -> Mel travels about with the Doctor (PROSE: The Deal - TV: Terror of the Vervoids) -> The Doctor briefly meets Mel (TV: The Ultimate Foe) > The Doctor drops her off (AUDIO: The One Doctor) -> The Doctor comes back for Mel (PROSE: The Ultimate Foe) -> Mel resumes traveling the Doctor (PROSE: The Quantum Archangel - TV: Dragonfire) -> Mel's various post Dragonfire stories (which aren't really relevant to this question but include her return to Earth, her reunion with Seven and Ace, and her becoming a CEO)


 * For the Doctor:


 * The Doctor briefly meets Mel for the first time at his trial (TV: The Ultimate Foe) > The Doctor drops her off (AUDIO: The One Doctor) -> Comes back for her earlier (PROSE: Business Unusual) -> Doctor travels about with Mel (PROSE: The Deal - TV: Terror of the Vervoids) -> The Doctor comes back for Mel after she is taken from her timestream by the Master to give evidence at his trial (PROSE: The Ultimate Foe) -> They resume their travels (PROSE: The Quantum Archangel - TV: Dragonfire) -> The Doctor's travels with Ace and all the rest (still ongoing today...)


 * (That's SUPER oversimplified and it's MUCH more complicated than that - note how I sorta glossed over directly referring to what actually HAPPENS in the story itself - and note that that was very purposeful and there's a good reason for it, but that's the sequence in very basic terms)


 * In a meta-sense, this would likely have been explained or addressed in the following season (or at least would have been more easily handwaved with "they sorted it out between seasons"), but Colin Baker's firing and replacement with Sylvester McCoy kind of put the kibosh on it.


 * Given that article 7 cannot be ignored, and the Doctor is definitely guilty of it, the inquisitor is remarkably quick to let the Doctor off.
 * He did just save her life, amongst others.
 * Is he, though? It's just been conclusively revealed that the whole trial was set up under extremely questionable circumstances and the Doctor has been subject to heavily manipulated and fraudulent evidence. Even the highly questionable legal system of Gallifrey would find it hard to justify continuing to detain the Doctor under such circumstances, at least not without making it even more nakedly obvious that it was a blatant attempt at stitching him up for something. In other words, after everything that's happened she's declaring a mistrial.


 * Just why does the Valeyard dress up as Mr Popplewick?
 * As the Doctor said it was a part of the Valeyard's nature
 * He's perhaps not literally dressing up as him; the point of the story is that the Valeyard has seized control of the Matrix and is manipulating everything to torment and attack the Doctor, and within the Matrix your mind makes things real to a degree. The Doctor is simply fighting back against the Valeyard's control of the situation by 'stripping away' the disguise of Mr Popplewick to demonstrate that it's the Valeyard underneath it; in the dreamworld of the Matrix, however, this is literalised by having the Doctor strip away Popplewick as if the Valeyard was wearing a disguise.


 * How does no-one notice the Valeyard switching places with the Keeper of the Matrix?
 * You really have to be looking for it to be the Valeyard as it is not incredibly obvious. (Intriguingly, when the Valeyard talks to the Inquisitor immediately before the reveal, it sounds like James Bree rather than Michael Jayston.)


 * No-one attempts to stop Mel entering the Matrix the second time.
 * Actually, the Keeper does by attempting to trip her again but was too early and Mel was expecting it. It can't be seen very well on camera.
 * It seemed quite obvious to me; right down to the look on the Keeper's face when he realised Mel had thwarted him.


 * Why does the Doctor take Glitz into the Matrix with him?
 * Like the Doctor said, two people make the Valeyard's job harder.


 * Why do they land at different times when they went through together?
 * There is a time difference between the real world and the Matrix as stated in TV: The Deadly Assassin when the Fourth Doctor has been in the Matrix for well over half an hour at least yet he is only in there for between 4-5 minutes as stated by Engin.


 * How do Glitz and the Master manage to escape the Matrix?
 * The Time Lords release them as the Doctor said.


 * Although Mel never directly heard the Doctor saying that the he opposed the evidence of the Matrix, the parts that she does here would be more than enough to give her that idea - so the Doctor's logic doesn't really work.
 * Sure it does. She clearly doesn't know definitively, which is his point.


 * The Valeyard should realise that if the Doctor dies, he will cease to exist.
 * The Valeyard is an amalgamation of the Doctor, not a definitive future.
 * The Valeyard is presumably trying to ensure his existence; if he takes over the Doctor in the past, he can make sure that his existence is guaranteed, rather than just existing as a potential future.
 * Also depends how he plans to kill him. The Valeyard may have intended a "merging" after the fashion of the Master/Tremas, thus taking over the rest of the Doctor's unused regenerations for his own evil purposes (though that still raises issues of time paradoxes, probably of little concern to a corrupt and desperate High Council and even less to the fundamentally warped Valeyard).


 * The Doctor says that he can't produce witnesses because they're scattered throughout time and space, but what about Leela?
 * There is no guarantee that Leela is still on Gallifrey, or even still alive, depending on the Time difference.
 * What could/would Leela serve as a witness? She wasn't present for any of the events in question. Even as a general character witness she wouldn't be all that useful since it's been several hundred years since she's known him and he's regenerated twice since then.
 * The Doctor is just speaking generally. Even leaving aside the points raised above, Leela is just one person; he's going to need many character witnesses and actual witnesses to rebut the video testimony the court has seen and prove that it's been faked, but they're scattered throughout time and are, without a pause in proceedings that the court is clearly not going to allow, essentially unavailable to him.


 * Why does the Master use the bauble to attempt to hypnotise Glitz, rather then his usual method of looking him in the eyes?
 * Maybe it wouldn't work, because Glitz is such an accomplished fast-talker and bluffer. ("I am the Master, and you" "Yeah, and I am Sabalom Glitz, I already know that much. Did I ever tell you about...") If so, the Master might already know or suspect this, or might even have tried to Master-eye him earlier.
 * The Master also uses the bauble in "Mark of the Rani", and also steals the Rani's mind-controlling parasites for an even more effective method of hypnotism. He seems to have lost the intrinsic ability to hypnotise (possibly as a result of being stuck with Tremas' non-Time Lord body), and has to rely upon artificial methods (as in "Time Flight" as well), deception, and brute force.


 * How is the Valeyard in the Sixth Doctor's timeline, when he is an amalgamation of the evil from either the Twelfth or last doctor?
 * The same could be asked about any multi-Doctor story (and, for that matter, the Watcher). It should also be mentioned that he is not the physical Doctor - but an amalgam - so different laws could apply to him.
 * Actually, aside from The Two Doctors, there's always some justification for multi-Doctor stories. In The Three Doctors Omega is creating havoc with in the universe and the time lords personally make it possible for the Doctors to meet up (and are only partially successful) likewise in The Five Doctors Borusa uses a time scoop to unnaturally gather the Doctor incarnations which is shown to be adversely affecting him (and once again it's only partially successful) and in The Day of the Doctor, The Moment uses all its OP powers to break time and cause a portal to open up in order to gather the incarnations. The Sixth Doctor era just didn't really attempt to justify anything like that and went with "the universe is small enough that you can bump into yourself every now and then."
 * The Valeyard has been specifically brought into this time period by the Time Lords for the express purpose of destroying the Doctor. They have presumably arranged matters so that he can exist in this part of the Doctor's timeline.