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"?
 * Not everything the Doctor told Martha was heard.
 * The Doctor had integrated with the Archangel network and could possibly send psychic messages to Martha.


 * 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.
 * Or perhaps they had been hypnotised into serving the Master, and the Doctor broke the hypnosis with his psychic attack.


 * How did Martha and the Doctor know when the countdown would take place?
 * They did not need to know when the countdown took place. They only needed to spread the word to use it.


 * 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 makes it 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.
 * 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.


 * There's a brief mention in one of the NSAs about the UK bending over backward for the Americans to "repair the special relationship after the Saxon incident", or something like that, and it's not hard to believe that at least some segments of the US government would be happier to leave the UK acting a little more obsequious than usual for the next few years than to push things more openly. Since we haven't seen every diplomatic meeting in the history of the Whoniverse, we don't know all of the details, but that's hardly a continuity error.


 * 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.


 * 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.
 * The Doctor had the device which locked the coordinates. He likely had a reverse function.


 * Wouldn't The Year That Never Was have coincided with Davros's reality bomb since it runs into circa May 2009?
 * Possibly. Whether the reality bomb was still created is unknown. It may have been as it's creation was not affected directly by any events of series 4 so would still have been created. However, if it was indirectly affected by any Doctor Who adventures as yet unchronicled, the bomb may not have been created.
 * How the Earth was stolen is unknown. It may have required infiltration by the Daleks, which the Toclafane may have detected. Whether the Earth was still of use is unknown also, as the Master was noted to have changed a lot of the landscape..
 * It's plausible that there was a little skirmish between the Master and his Toclafane vs. some Dalek scouts, and the Daleks were chased away… shame we didn't get to see it, though…


 * The Daleks may have noted that Sol 3 was "closed for business" and used another planet, such as the one that would become New Earth.


 * Additionally - this is not necessarily another dimension, but a paradox generated within one - and this potentially negates the effects of the bomb.


 * Also, history changes. Once there was a 2009 with neither the Master nor the Reality Bomb. Then the Master changed history, creating a second 2009. Then that was undone, restoring the original 2009. Then Davros changed history, creating a third 2009, which wasn't undone.
 * Well, not until the cracks, which created yet another 2009… But the point stands.


 * 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.
 * On multiple occasions, he's expressed affection for the TARDIS's police-box appearance. Donna ended up with the Doctor's mind and knew how to fix it, so the Doctor does know how to fix the circuit, but chooses not to.
 * As The Eleventh Hour has shown, the TARDIS repairs itself after significant damage. Perhaps this is what happened here, except without an appearance change.


 * 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.


 * It is possible Time Lords can survive shots to the head and start regeneration within microseconds.


 * The ruse was so that Martha was caught at the right place at the right time.


 * The Master didn't have to believe it was a credible threat, he just had to believe that Martha might think it was a credible threat.

First thing, this isn't new information, for crying out loud, that is what the doctor has been saying since, we first saw the master, back in the Third Doctor's time.
 * How come the Doctor mentions how him and The Master grew up as children on Gallifrey together? In the Doctor Who Special 'The Five Doctors', the First Doctor fails to recognise The Master when they meet, so this means they could not have grown up together?

Second, the only reason that they didn't recognise each other is because, at this point the master is inhabiting a stolen body.
 * How exactly did the Time Lords resurrect the Master when he was sucked into the Eye of Harmony in the 1996 TV Movie?
 * That isn't a plot hole. It's just something we don't know. And since the Eye of Harmony links back to Gallifrey, it would probably be quite easy.
 * If you've read The Gallifrey Chronicles, you should understand why it shouldn't be too hard to resurrect him on Gallifrey through the link; if you haven't, it's too hard to explain.


 * Alternatively, in The End of Time, the Cult of Saxon were able to resurrect him with just the DNA from Lucy's lips and the technology available to determined human beings, so it probably isn't as hard as you think. Consider that they had his Matrix records, whatever was left behind in the Tremas (or post-Tremas NA) body after he transfered his essence via deathworm, and whatever echoes were available in the link. And they had biological super-geniuses like the Rani and even Rassilon to work on it.


 * But if this is the case, and the Eye is the TARDIS' power source (or 'soul', whatever), how can it still work after Galllifrey's destruction?


 * It doesn't. That's why the Doctor refuels at rifts, as RTD explained in… either DWM or an Annual.


 * By the way, the Heart is its "soul", not the Eye.


 * Can the TARDIS still work?


 * Yes, but only because the Doctor refuels at rifts.


 * (if so, going even further, does the Eye still link to Gallifrey, bypassing the Time Lock?)


 * That's a good question. But the last time Gallifrey was erased, even without a Time Lock, the TARDIS ended up with a link to nothing, which caused all kinds of negative consequences in the later EDAs. Presumably something similar would happen here—but, since both the Doctor and the TARDIS have already been through that once before, you can assume they would have found some way to close off the link safely.


 * Actually, all of those problems could have been caused by the fact that the Master was stuck living in the middle of the link, powered by all of the singularities in the universe. The Doctor thought it was the lack of Gallifrey on the other side that was the problem, but that's before he found out about the Master. And he was wrong about tons of other stuff through those novels.


 * Why did Jack bother telling the Doctor and Martha that he used to be called the Face of Boe?
 * The best guess is that he'd heard them discussing the Face of Boe. The reason he waited until he was leaving to tell them could be because he didn't want them grilling him on it until he had a chance to work things out for himself, but it also could be because he thought it was a meaningless coincidence and was just being funny.