Theory:Doctor Who television discontinuity and plot holes/Logopolis

• When Nyssa objects to the Doctor collaborating with the Master, the Doctor states "I've never chosen my own company." but in the very first Doctor Who (DW: An Unearthly Child ), he CHOSE to kidnap Barbara and Ian. Susan pleaded with him to let them go.

The Doctor is speaking generally, reflecting on how he oftend ends up in the company of certain people rather than selecting to have them with him. Recent to that time in his life, Romana, Adric, Tegan, and Nyssa could all be described in such a manner. If you really want to think of it as such, you could even argue that the Doctor felt forced to "kidnap" Ian and Barbara, because he feared the consequences of letting them go and potentially tell others of him and the TARDIS.

• This story features the Doctor's TARDIS materialising around the Master's TARDIS and creating a gravity bubble and the recursive phenomena of infinite TARDIS'es nesting within each other. Two TARDIS's materialised "inside" each other in DW: The Time Monster, but did not happen when the TARDIS materialised inside Professor Chronotis's rooms (actually his TARDIS in disguise) in the untelevised DW: Shada.

Chronotis's room was not a complete TARDIS; it was not dimensionally transcendant.

• Why does the policeman take the doll-like corpses so seriously?

Because he recognizes one of them as being the first constable seen in the story.

• Surely the Doctor's plan of flooding the TARDIS to flush-out the Master is absurd nonsense.

The Doctor was feeling very fatalistic at this point. It is doubtful there is a normal procedure of what to do when your arch-nemesis creates a gravity bubble within your TARDIS.

• Tegan appears amazingly reconciled to the extraordinary events happening around her. In particular she does not appear to comment on the size of the TARDIS. She witnesses the regeneration of the Doctor without any evident wonderment and without questioning what is happening.

Different people react to extraordinary events in different ways.

• The only indication that the Watcher is the Doctor's future self is Nyssa saying, 'so it was the Doctor all along'. But how does she know?

As he is merging with the Doctor laying on the ground, she works out that it must be the Doctor.

• It is never really explained how/why the Watcher has come into existence for this regeneration and not previous or future ones.

It's a process that is not always necessary. It's been rather clearly shown that the Doctor does not have the smoothest time with regeneration. Sometimes he needs a little help, even if from a future part of himself.

• If the Watcher is the in-between point of the Doctor's regenerations and has foreknowledge of what will happen to Doctor #4, then why didn't he warn the Doctor against going to Logopolis in the first place? Knowing that the Master is stalking the Doctor and indulging in a totally random killing spree, and that the Master will follow the Doctor to Logopolis and set in motion a chain of events that will erase a portion of the universe and kill countless beings....why doesn't he try to prevent this from happening?

The third part of the Blinovitch limitation effect, prevernts time travelers from messing around with their own history.

• The lock on the Master's TARDIS changes place in part 1.

A functioning chameleon circuit is more than capable of changing the location of the lock.

• In Part 4, the Master's TARDIS materialises just before the worker leaves the room, Surely the worker would have heard it?

A TARDIS is meant to blend in, and we now know that they can also have perception filters. Additionally, we don't know how loud the materialisation sound was at that moment, how good the worker's hearing was, or if he would have dismissed such a sound as something else (such as a piece of equipment).

The worker is wearing headphones.

• When Adric and Nyssa are "outside time and space", how can they possibly see things that change with the passing of time - i.e. the growing entropy field?

The TARDIS scanner could show them the areas of Space-Time in which they were interested, much as the Time-Space Visualiser could in DW: The Space Museum and The Chase

• Why does the Doctor have a flashback of the Decaying Master when he's just met the new one?

He is having memories of various moments of his incarnation's life. Why shouldn't that include the version of the Master which he encountered on Gallifrey?

• Why is there a litter bin next to the 'Take Your Litter Home' sign in episode one?

Such signs are common in some places as a reminder that you shouldn't be depositing large amounts of trash into such bins if possible.

• Exactly WHY are Block Transfer Computations spoken aloud?

It's probably helps the Logopolitans focus their minds on the computations by speaking them. Sort of the same rationale for why some people think better by talking to themselves.