Theory:Doctor Who television discontinuity and plot holes/The Mind of Evil


 * The Doctor fears Koquillion and War Machines yet in their featured episodes, he had no or little fear of them.


 * There is a difference between not showing fear, and not feeling it on some level.


 * The War Machine could be taken as symbolic of WOTAN (which highly unnerved the Doctor by knowing more about him than it had any right to) and of the Doctor's general dislike of sentient technology (of the non-dog-shaped variety, at any rate). The Koquillion mask (Didonian ceremonial garb) could possibly be taken as symbolic of the dark past of Dido, which had clearly not always been a peace-loving place (bearing in mind its tiny population, and the sinister traps still remaining in its caverns). Not to mention Bennett did actually come quite close to strangling him, but for the Didonian survivors' timely intervention. Must have been a fairly scary moment ...
 * The very first time the Doctor sees The Post Office Tower, he is gripped with fear.


 * There is also the fact that Bennet was clearly amongst the most evil people the Doctor has ever met, even amongst the many tyrants and monsters he's encountered in his long life, few would have been willing to commit such a brutal act of genocide with such casualness.


 * The destruction of the 'deadly' Thunderbolt missile at the climax of this story seems to do surprisingly little damage to the surrounding area.


 * Destruction of the missile itself doesn't automatically mean detonation of the payload, especially with nuclear missiles. At any rate, Thunderbolt has a poison gas warhead and a nuclear-powered rocket engine. The explosive contents of the actual warhead / detonator are not mentioned, but presumably they are only sufficient to ensure widespread distribution of the poison gas and not massive ground-level destruction (Indeed, it sounds like a weapon designed to kill people and leave buildings and property mainly unharmed).


 * How does the water get into the drowned man's lungs if he's only killed by his fear of drowning.


 * The fears are physically manifested as well, as explained in the story.


 * During a fight sequence in which water is spilled, the Master twice slips in the puddle.


 * This may have been intentional on the actor's part.


 * How would it be a plot hole that someone would slip on a wet floor? Seems perfectly normal.


 * It's just a mistake during recording that was left in probably because of lack of time.


 * I recall reading that Pertwee noted the water spill and considered breaking off, but imagined the director wanting it left in. His instincts were right.


 * Is it normal military procedure to simultaneously transport a missile, the missile's warhead, and the missile's fuel in the same convoy? That seems like an unnecessary security risk.


 * Budget cuts?


 * Probably not, but it was being transported through their own country, and the risk of anyone stealing it seemed next to nil (as they were unaware of The Master's plans). It's possible it was decided that it would not be worth the extra cost to transport them separately.


 * Some of the dialogue in Episode One implies that the Master has spent almost a year establishing the whole Emil Keller alias by getting his machine used in Switzerland, etc. But as I understand it, The Master's 'master plan' in this story seems to be to orchestrate the prison takeover as a means to hijacking the Thunderbolt so as to destroy the peace conference and plunge the Earth into war. That being the case, why is he bothering with the Emil Keller identity and the whole Mind Parasite angle? Surely not simply as a weapon to take out a few diplomats at a conference he is planning to blow-up anyway. As a plot-strand it just seems extraneous.


 * He has been lying low and using his alias as a means of getting criminal brains for the Mind Parasite to leech, in the hopes of using it as an easily controllable weapon. This turned out to be a bad idea ... He has now changed his plans and aims to seize a less treacherous weapon, albeit while still using the Mind Parasite for a bit of highly risky leverage.


 * I see what you mean. It seems to me none of the Master's behaviour makes sense unless you assume his primary objective is entertainment. He is, in essence, a man who finds himself trapped on what he considers a very boring planet, who decides the best way to pass the time until the next ride home is to find entertaining ways of destroying it. The Master probably concocted the Prison Break/Missile Plan as much because it appealed to his sense of drama as from any more practical considerations.


 * If you are scraping round for a motive for the Master's desire to blow up the world, he himself usually cited the fact that he did what he did out of a desire for revenge on the Doctor: he wanted to destroy the Earth because it was the Doctor's favourite planet.


 * How does the Master know that it is the Doctor's favourite planet? That was said years later, by Tom Baker's Doctor. Pertwee's Doctor disliked his exile on Earth, and was constantly trying to escape (in particular, by stealing the Master's own dematerialisation circuit, which he still had in his possession in this story).


 * The Master and Doctor knew each other long before Terror of the Autons, I'm sure they talked about many things including Earth. The Doctor would prefer to be a free man, he loves Earth, but doesn't want to stay there!


 * It had been established in the previous serial, Terror of the Autons, that the Master's TARDIS is no longer working. Indeed, in Mind of Evil the Master actually recovers his missing circuit at the end of the final episode: this is a major plot point in that episode. However, in Episode 1 the only practical way in which the Master could have impersonated Emile Keller (to install the Keller Machine at Stangmoor Prison a year earlier) was to have gone back in time by a year, using his TARDIS - which is not functional at that point.
 * He presumably set up the Emil Keller identity and started that plan at some point before (or during) "Terror of the Autons" as a back-up plan.


 * Why does the Master bother to set up the elaborate scheme for murdering the Chinese delegate, so as to sabotage the peace conference, when he is arranging to destroy the conference with the Thunderbolt missile? Put another way, why is he going to so much trouble to hijack the missile (involving seizing control of the prison, and installing the mind parasite in the Keller machine there), when he is so close to breaking up the peace conference by the simple expedient of murdering the delegates? These two aspects of the Master's plan are irreconcilable: either plan, on its own, is sufficient to achieve the Master's goal, so the other is redundant.
 * Essentially, he has a Plan A and a Plan B going. Plan A is to sabotage the conference by murdering the delegates. If that fails, however, then he's got Plan B -- blowing them up with the missile -- in his pocket just in case. It's unnecessarily convoluted but, as another Time Lord memorably will say in a later episode, the Master is the type of person who would get dizzy if he tried to walk in a straight line.


 * With his TARDIS out of action, how does the Master travel to the unnamed alien planet and collect the mind parasite? This unresolved problem is carefully side-stepped at every point: the Doctor is never allowed to consider where the creature actually comes from.
 * The mind parasite was already in the TARDIS when he materialised in the circus car park.


 * Why does the Master need a huge gang of criminals to hijack the missile, which he knows has a minimal escort, instead of simply adopting his usual technique of hypnotising the tiny UNIT force escorting it (as he did in the following serial, The Claws of Axos)?
 * It takes time to hypnotise individuals one by one. He would have been over powered before hypnotising the last soldier.


 * Why could he not have hypnotised them at UNIT HQ before they set out, in a similar manner to his actions in The Claws of Axos?


 * Because he either didn't think of it or didn't have the opportunity. As stated in the OP, "The Mind of Evil" comes before "The Claws of Axos"; it's hardly unreasonable that he came up with the idea after these events, or simply decided on taking different approach after this one failed, or took advantage of an option or opportunity that wasn't immediately available to him in the earlier story.


 * How does the Master know, a year in advance (when he installs the Machine), that the missile's route from its Army storage facility to the dumping site at sea will take the convoy close to Stangmoor Prison? If he is relying on stolen information from the Time Lords' files (as in Colony in Space), how does he obtain it with his TARDIS out of action? And the fact that he goes to the trouble of eavesdropping on UNIT's communications implies that he does not know the convoy's route at all. These facts are irreconcilable.
 * It was a secondary plan.
 * But where does he get his knowledge, a year previously, that the missile convoy will pass close enough to the prison to make it worthwhile introducing the Keller machine into the criminal justice system?
 * The Master, like the Doctor, is a time traveller. He has presumably gained a lot of information from the future that he can use in concocting his schemes. He eavesdrops on UNIT's communications simply to ensure that his information is correct. He could have gained that information at any point during his travels before "Terror of the Autons" and used it to base his plans on.
 * As for how he accesses the Time Lord files (or, indeed, any information from the future), that simple -- he got it at some point before his TARDIS was sabotaged and downloaded it into his TARDIS' computer systems. His TARDIS can't travel through time, but presumably the information databanks and computers are still working okay.


 * Why is the Doctor suddenly and unaccountably interested in prison reform, such that he attends the demonstration of the Keller Machine in Episode 1? This is not a subject on which he shows interest in any other serial: not even in the one other serial, The Sea Devils, which explicitly involves a prison. Also, if he sees the Keller Machine as a threat, why has he not investigated the process during the year-long trial which has already been running?
 * Why not? He's UNITs scientific advisor with privileges. The Brigiadier may have told him, or he may have become interested because he was bored living on Earth.


 * But why then does he express no interest in prison reform during The Sea Devils?


 * Because unlike the inmates of Stangmoor Prison, the Master is imprisoned in rather cushy circumstances wherein he is not being subject to rather questionable mental programming techniques. His prison doesn't need reforming (if anything it is, as events demonstrate, rather too lenient), and so the Doctor has no real reason to bring it up. Aside from involving a prison, the situations are quite different.


 * As for why the Doctor hasn't investigated the Keller Process up until this point, this is almost certainly the first opportunity he's had to do so. Experiments which are in the trial phase usually don't have a lot of access for people outside the experiment and aren't really discussed that much, precisely because they're undergoing trials and those involved don't want to talk them up too much in case those trials fail. The Keller Process has presumably only relatively recently become both public enough for the Doctor to be made aware of it and public enough for him to be able to gain access to investigate it further.


 * Why shouldn't the Doctor show some interest in prison reform? He's been demonstrated to have lots of interests and knowledge on a wide range of topics, and frequently and actively gets involved in matters involving justice, freedom, oppression, etc -- concepts which prison reform tends to revolve around. It just doesn't come up very much because the show isn't about prison reform by itself, and because the Doctor tends to get distracted by one of the many other interests / problems he ends up facing.


 * Also, the Doctor's never been exiled to one location on one planet before. He has presumably decided to take an interest in some of the political and social issues in Britain and Earth in general if he's going to be spending a prolonged period of time there; he just so happens to be taking an interest in prison reform here. For all we know he continues to take an interest in it, we just don't see it because it doesn't intersect with any of his other adventures and so never really comes up again.