Theory:Doctor Who television discontinuity and plot holes/Last of the Time Lords


 * How did the Doctor know about the countdown a year before it was due?
 * The Master is predictable, so the Doctor knew that he would never resist the temptation of having a "ticking clock" as part of his plan.


 * In The Sound of Drums, the Doctor tells Jack that he shouldn't touch the paradox machine, as it could destroy the solar system. So why does he carelessly shoot at it with an Assault Rifle?
 * When the Doctor warns him, he doesn't know what the paradox is yet. Once he knows what the paradox is, he probably determines that it's safe to destroy the machine. Furthermore, it's not as if they had much choice at that point, as all six billion Toclafane were rushing towards The Valiant.


 * How did Martha know to walk round the Earth for a year based the Doctor telling her "use the countdown"?
 * It's probable that her sources recently told her that the countdown was coming. Not every word the Doctor said to Martha is revealed; the Doctor could have told Martha at least 10-15 seconds of information. It's also been established that the Doctor can impart (and remove) information through psychic means, so he may have given her far more information than was actually spoken. After all, the Doctor reveals he integrated himself with the Archangel network.


 * How did the Master know about Rose absorbing the time vortex?
 * The Doctor told Jack about Rose absorbing the time vortex near the end of Utopia, when Jack was in the radiation room, and Professor Yana heard them over the intercom.


 * Why did a soldier who had been loyal to the Master decide to obey Jack Harkness' orders?
 * They are only loyal to the Master under duress.


 * How did Martha and the Doctor know when the countdown would take place?
 * The Doctor would have known about the countdown and either told Martha before she teleported down to Earth or transmitted the thoughts through what was left of the TARDIS psychic network. Also, it could have been an undisclosed known notion, learnt by Martha as she was peregrinating throughout the world.


 * If the Master was able to convert the TARDIS into a paradox machine in order to change history, what's to stop the Doctor using the same kind of machine to allow him to change the events of the Time War?
 * The Doctor is clear that the Paradox Machine is not a good or safe thing. The Time War involved all kinds of temporal mayhem that could make use of a Paradox Machine to affect it even more difficult and dangerous. Also, The End of Time explains why the Doctor would have good reason not to prevent the destruction of Gallifrey even if he could do so.


 * When the Master talks about the Doctor's achievements, he mentions the Medusa Cascade and how he sealed it, this does not occur until Journey's End, so how did he know?
 * He is referring to an earlier case of the Doctor sealing that rift. The Doctor himself mentions in The Stolen Earth having been in the Cascade before, when he was 90.


 * Apparently the president of the USA is killed (by the Toclafane) and this is recognised post-time reversal. Wouldn't that cause international outrage the likes of which we would see a different ending?
 * This may have been tempered by the subsequent death of the Master. In addition, it would almost certainly have been discovered thereafter that he hypnotized Britain into electing him.


 * Jack refers to himself as the Face of Boe, apparently without realising the connection to the Doctor's "old friend". But wouldn't he have known about the Face either through the events of Utopia in which the Doctor realizes the significance of Boe's final message (per Gridlock), or even before that given the Face was something of an interstellar celebrity in Jack's home era (per The Long Game)?
 * The Long Game is set well after Jack's home era. The Doctor never told Jack about the Face of Boe, and Jack probably teleported out of the year 200,100 without checking intergalactic celebrity news. It's also possible that he was given the nickname in honor of the Face and later became the Face himself in a case of paradoxical irony.)
 * In "Utopia", he overheard Martha speaking about the Face of Boe and displayed no reaction. Perhaps he's just joking as an afterthought, toying with the Doctor's expectations.


 * What happened to all the people who were on the Valiant when the President was assassinated but not present when the Paradox Machine was destroyed? To go one step further, what about the Toclafane vanguard who assassinated president Winters? Does that mean they are still on the loose? As the Valiant was rewound to where it was before, anyone on the Valiant at the time of assassination but not at the destruction of the paradox machine would have been killed (or rather stop existing). One step further, however, anyone NOT on the Valiant at the assassination but on it during the paradox machine's destruction should have been duplicated. How can all this be addressed?
 * Fortunately we don't know of anyone that was on the Valiant when the paradox began and not when it ended, except the Toclafane that killed Winters, and we don't know of anyone that was not on the Valiant when the paradox began and on it when it ended.


 * It has been established that the First Doctor was his first incarnation and would have been over 800 years old, and he only appeared to be an old man, so why is that when aged by as little as a hundred, the Tenth Doctor becomes as aged as he is shown?
 * An effect of artificial aging, as seen in The Leisure Hive. The Master has unnaturally made the Doctor age more like a human.


 * The Doctor says that time has reversed to "just after the president was assassinated but just before the spheres arrived", so what killed the president?
 * The Doctor meant that it was before the scene shown where the sky splits open and all of the Toclafane pour out. Not the scene where the Toclafane first appear and kill President Winters. Also even if Toclafane from the split had killed him unless they were on the Valiant they would have been sent back to Utopia. The Valiant's position is the 'eye of the storm' so that the people aboard it still experienced the year 'which never was'. The Toclafane which killed him were not on the Valiant so they didn't make it.


 * How did the Doctor repair the TARDIS when the Doctor wasn't worried that the Master could repair just the navigational systems and the Doctor had a lot more to repair?
 * The Doctor is more familiar with his TARDIS and they do share a telepathic connection so he could have found it a lot easier to fix it.


 * Wouldn't The Year That Never Was have coincided with Davros's reality bomb since it runs into circa May 2009?
 * Yes, it probably would have, however, since Earth had been fitted with a vast number of misiles that also contained black hole converters, the Daleks may have thought it better to avoid the planet as even they couldn't withstand that kind of firepower. As a result, they may have just used different planets for the reality bomb.
 * And had not gotten around to detonating it before time was reversed, thus it effectivly never happened.


 * It isn't explained how the Doctor converted the destroyed paradox machine back into the TARDIS. How did he repair it so fast?
 * He's frequently shown expertise in manipulating and repairing the TARDIS, and the re-conversion may be deceptively simple.
 * But he hasn't been able to fix the chameleon circuit for years which is just one part of the machine.
 * He hasn't been trying particularly hard. On multiple occasions, he's expressed affection for the TARDIS's police-box appearance.
 * As "The Eleventh Hour" has shown, the TARDIS repairs itself after significant damage. Perhaps this is what happened here, except without an appearance change.

Maybe but Martha doesn't know this. Also it would obvoiusly make him far more vunrable, as it is unlikely that any of the slave workers have guns, and plenty of ammo, plus they are surprised when he land's every one acts surprised, surgesting that even if they did, they wouldn't get a chance to be close enough to him.
 * Even though the Anti-Regeneration gun is a ruse wouldn't it be pointless since if the Master was suddenly killed (such as suffering a direct shot to the head) he would permanently die and Regeneration would not be possible.