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.


 * 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 legal system of Gallifrey would find it hard to justify continuing to detain the Doctor under such circumstances. 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


 * 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 does 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.


 * 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 cant 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 regenerate twice since then.


 * 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 bluffster. ("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 doctors time line, 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."