Theory:Doctor Who television discontinuity and plot holes/Terror of the Autons

Why do the Time Lords confine themselves to simply warning the Doctor about the Master's arrival rather than arresting and trying him? Surely his actions are no less criminal in their eyes than the Doctor's.

''              The Time Lords often have ulterior motives, which involve letting events play out with minimal interference on their part. ''

''                          Also, keep in mind that The Time Lords weren't able to track down The Doctor till he called them to deal with the War Lords. It could be they have no way of knowing The Master's whereabouts, just that he's headed for Earth. They may have been planning to arrest him, but he keeps escaping before they can get there.''

In episode one the Doctor could have got to the volatizer by hopping in through the open window (which is how the Master must have got out having set the trap).

"The Third Doctor always likes to do it the most 'Secret Agent' way."

The Doctor intuitively leaps to the conclusion that Jo is opening a bomb at the end of episode one.

At the start of episode three, neither Auton policeman is killed, but only one returns to the Master and Farrell. What happened to the other one?

                 (The fact that we only see one on screen doesn't mean that the other isn't elsewhere nearby.)

Why does the Master try to blow up the radio telescope anyway? He needs it in order to carry out his invasion plans.

                   (He claims that he didn't expect it to actually kill the Doctor, and refers to it as a "calling card" of sorts. Had it actually worked, he would've undoubtedly been delighted at the death of the Doctor and happily found a similar facility to carry out that part of his plan.)

The Doctor tells Yates to stand back while he defuses the volatizer. He might have clarified just how far back to stand. He says later that the volatizer had the destructive capability of a 15-megaton bomb.

''                  In human technology at least, some larger explosives contain a smaller detonator charge. Even if the larger explosive is neutralised, the smaller detonator could still go off and hurt someone standing nearby.''

Jo can't remember where she heard the voice that told her to set off the bomb. The Master only told her to forget meeting him. She was supposed to remember meeting Mr. Farrell and to return with a negative report, that everything was in order.

(This is consistent. She remembers meeting Farrell, but it doesn't stand out from all the other plastic facilities she visited that day. She doesn't know which one she met the Master at.)

The Doctor discovers that carbon dioxide from the lungs dissolves the film that the daffodils shoot at people's faces, ostensibly explaining why the film was not found on any of the victims. If that's true, why didn't the victims' own breath dissolve it in time to let them breathe again? If it's a delayed reaction, then the victims would already have suffocated and not have had any breath left to dissolve the film.

The stuff probably absorbs the carbon dioxide then after a while it dissolves.

How does the Master disguise himself as someone of a different height? And, indeed, why disguise himself at all?

(Disguising himself is prudent. He can't be sure how much UNIT knows, and therefore if someone there might be able to recognize him. His hypnotic ability is one method at his disposal to have also appeared taller to those he met. 

Also, a true master of disguise can appear to be a different height, at least to some extent, and of course it's easier to appear taller than shorter.)