Theory:Doctor Who television discontinuity and plot holes/Day of the Moon


 * At the end of the first episode Rory and River are clearly in trouble... yet no mention is made of how they got out of the pseudo-TARDIS?
 * They weren't in that much trouble. As we learned later, the Silence rarely act directly; instead of killing the two right there, they'd just make plans at their leisure for the human authorities to take care of the "terrorists" later, in a way that would raise no questions and require little effort.


 * Never-minding that two people probably couldn't lift a rock of dwarf star material, where did the US government get dwarf star material in the first place if they're just now getting to the moon?
 * Planet Earth has dealt with numerous of aliens and especially alien technology. Secret organisations such as Torchwood were up and running at the time. Earth is educated in many things alien. They only went to the moon because the Silence edged them too.
 * Since the prison was actually part of the Doctor's plan, he may have told them where to get it.
 * They are at Area 51. They probably have lots of alien technology there.


 * Why was the Doctor captured and Amy, Rory and River hunted down? If they were working for the President, surely nobody would capture them and lock them up?
 * This was most likely part of the Doctor's plan in order to gain intelligence on the Silence.
 * And to keep the Silence off their trail. The Silence wanted to eliminate them, and Delaware was able to fool them into believing he was doing it for them. Only he, the Doctor, and Nixon knew any different.
 * Alternatively, the Silence were influencing the FBI to pursue the group.


 * The Doctor put the device in Apollo 11 before he received the video of the Silent and before he even knew what it was going to say. Why would he set it up?
 * Canton was probably trying to make The Silent order their deaths. It was the plan.


 * How come The Doctor, Amy, Rory or River don't try to kill The Silence on sight? They must have seen the Lunar Landing.
 * The post-hypnotic command was never in the footage they saw in their own timeline.


 * Why didn't the Doctor sense that the Little Girl was a Time Lady?
 * The Doctor can't always sense a Time Lord or Lady if they are not synchronised with his time line, for example, The Master during Series 3.
 * The reason the Doctor couldn't sense the Master was because of the Archangel Network, not because there timelines weren't synced. Until we know the full nature of the little girl, we don't know for sure that the Doctor should have been able to sense her.
 * The space suit the Little Girl was in was composed of "at least 20 races of alien technology", so because of all that stuff (and the fact that space suits are supposed to be air tight), he probably couldn't smell her, since she was out of the suit before the Doctor got to it.
 * We don't know for a fact that the Little Girl is a Time Lady.
 * 'Smell' is probably a very literal way of looking at Time Lord's sensing each other (despite the odd emphasis on it in End of Time) as the Doctor expects to detect Time Lords on the other side of the universe doing this. But as above, we don't know the girl is a Time Lord.
 * This particular Doctor seems to interpret 'smell' (and 'taste') more literally than most....
 * It's always possible that the Doctor _did_ sense that she was a Time Lady, or that she was whatever else she might turn out to be, or at least that he sensed that there was something special going on that he couldn't quite figure out. He calls out the mystery at the end of the episode, after all.


 * What happens to all the bodies of the dead Silence that are (presumably) killed by the humans in the open?
 * Buried? Burn? Whatever the human race normally does with alien bodies.
 * Exactly. Wouldn't the discovery of dead aliens littering the planet cause disruptions in the timeline?
 * It wouldn't if no one could remember seeing them.
 * So where does that leave the bodies? Do they just lie there and decompose?
 * The Doctor explicitly told the Silence that if they were smart, they'd run as fast as they could. It's not like they're Zygons who believe that backing down from a plan is equivalent to suicide, or Sontarans who would actively prefer to go down in battle than to retreat. Even if they pooh-poohed the Doctor's warning at first, they would have realized he was right pretty quickly, and gotten off the planet or gone into hiding as fast as they could.


 * If the Silence have been guiding the human race's technological development, couldn't destroying the Silence cause a decline in humanity's technological growth?
 * It was stated by the doctor that the Silence don't create things by themselves, they act as a parasite and steal human technology. Humanity is still a naturally creative, and inventive race.
 * It can probably be assumed the Silence make specific nudges depending on what they need at the time, rather than spurring humans to motion in general.
 * If the earlier Doctor arrived in the Tardis from his timeline, wouldn't the older (dead) Doctor's Tardis be left in 1969?
 * No, it would be left in 2011.
 * Which still leaves two questions. Firstly: Where is that Doctor's TARDIS? Secondly: What happens to a Timelord's TARDIS when they die?
 * "There is a cemetery of dead Tardises at the end of time" Read on the website, if I'm not mistaking. It is probably going to commit "time-suicide" or something like that.
 * 200 year older Doctor dies, he arrived in the Tardis with Amy and Rory, 200 year younger Doctor arrives in 1969, wouldn't he be surprised that Amy and Rory were there already? Or would he assume River Song brought them? The younger Doctor leaves with Amy and Rory in his Tardis, but the future Doctor's Tardis would be left where Amy and Rory exited it. Would this create a paradox?
 * The younger Doctor meets them in the diner in 2011 after the older Doctor dies in 2011. THEN they travel to 1969.
 * Does the TARDIS have some kind of "perception filter" which causes people to not really notice it (like Prisoner Zero) or forget it (like the Silence)? In "The Parting of the Ways", the Doctor sends Rose back to Earth in the TARDIS when he thinks he is going to die. He tells her to just "let the TARDIS die", and to leave it where it lands, confident that "No one can open it, no one will even notice it."
 * 200 year older Doctor dies, he arrived in the Tardis with Amy and Rory, 200 year younger Doctor arrives in 1969, wouldn't he be surprised that Amy and Rory were there already? Or would he assume River Song brought them? The younger Doctor leaves with Amy and Rory in his Tardis, but the future Doctor's Tardis would be left where Amy and Rory exited it. Would this create a paradox?
 * The younger Doctor meets them in the diner in 2011 after the older Doctor dies in 2011. THEN they travel to 1969.
 * Does the TARDIS have some kind of "perception filter" which causes people to not really notice it (like Prisoner Zero) or forget it (like the Silence)? In "The Parting of the Ways", the Doctor sends Rose back to Earth in the TARDIS when he thinks he is going to die. He tells her to just "let the TARDIS die", and to leave it where it lands, confident that "No one can open it, no one will even notice it."
 * Does the TARDIS have some kind of "perception filter" which causes people to not really notice it (like Prisoner Zero) or forget it (like the Silence)? In "The Parting of the Ways", the Doctor sends Rose back to Earth in the TARDIS when he thinks he is going to die. He tells her to just "let the TARDIS die", and to leave it where it lands, confident that "No one can open it, no one will even notice it."


 * Canton states that no signal could get through the walls of the Doctor's prison, but he sends the recording of the Silence to the Doctor and to Apollo 11 from inside the prison.
 * He left the door open.
 * and even if he didn't leave the door open, he is probably using a "super-phone" which can get signal anywhere as seen in "World war three"
 * I was going to say - cell towers in '69?
 * Canton didn't send the video directly from Amy's phone, he pressed play and then clamped it onto some kind of transmitter which looked like the one the Doctor installed in the lunar module.
 * I was going to say - cell towers in '69?
 * Canton didn't send the video directly from Amy's phone, he pressed play and then clamped it onto some kind of transmitter which looked like the one the Doctor installed in the lunar module.


 * If Amy was with the silence and didn't remember the last few days she was locked up with them how did she remember calling Rory 'stupid face' and leaving him that message
 * We don't know how much Amy remembers, but if she didn't see the Silence while she was leaving the message, she may still remember it.


 * How did The Doctor and his companions leap from never remembering The Silence in episode 1 to actively keeping record of and going after The Silence in episode 2?
 * There was a three-month gap in-story between the episodes. My guess is that when the Silence attacked at the end of TIA, the group escaped, realized that had been attacked but couldn't remember anything about the attackers, and then went about trying to discover the attackers.


 * As much as I like your hypothesis, it still is just a hypothesis and is thus still a huge plot hole.


 * ...and that you for specifically pointing that out . My point is that the Doctor and his companions had to have developed some awareness of the Silence, and that awareness motivated them to seek the Silence.


 * Isn't this section for people pointing out plot holes and people correcting the plot holes by pointing to something that happened in the show that explained said plot hole... not people giving their own independent theories?


 * No. This is a place where we attempt to explain supposed plot holes. Theories are valid here, as long as they are not too far out there.


 * Remember that Amy took a photo of one in the White House, and that you are aware of the Silence when you are looking at one, in addition to recalling all your previous sightings and encounters. If Amy saw the photo on her phone, as long as someone was looking at it they would be aware of the Silence and that they had seen them in the warehouse. As soon as they looked away they would forget, but while looking at the photo they could have formulated the plan to "tally" the sightings.
 * Also remember that at one point near the end, the Doctor specifically tells them to keep one Silence in sight at all times. Presumably they've done this before--maybe even using the hologram--to make it possible for them to make their plans.


 * In the episode 'Blink' the doctor and martha are stuck in 1969 and state they have watched the moon landing four times. Does this mean the doctor must have already seen the silence ordering everyone to kill them? Also does this mean there were two versions of the doctor in 1969?
 * The Doctor has traveled to many of the same years / dates as previous incarnations of himself, he just tries to make sure he doesn't run into those incarnations. That said, this is just an instance of the Doctor rewriting history. His previous selves haven't experienced this particular timeline, and the Doctor is known to rewrite history every now and again and since his living timeline isn't linear, being a time traveler, his previous selves would be unaffected by the change.
 * Also, in "Blink" when they said that the watched the moon landing, i think they meant that they watched it live from the moon not on TV. That's what made it special for them. Otherwise they could've watched in on TV in any other year not 1969. So if Martha and the Doctor were physically on the moon during the moon landing, then they didn't see the Silence since it was only on TV.
 * Your additional point is rendered moot as Martha (and any of the other new-who companions) would have seen recordings of the famous moon landing a few times in their lifetime. The previous point of the Doctor's timeline not being linear still stands.
 * For that matter, most of the old-Who companions would have seen it, too. Only the first 6 seasons of the show were before 1969, so everyone from Liz Shaw on (and that's even if the UNIT stories weren't set in the future--she started in 1970) would undoubtedly have seen the moon landing (except for a few special cases like Leela). (And, even from the first 6 seasons, Vicki, Steven, and Zoe were from the future.) But so what? Maybe Liz Shaw and UNIT had seen the Doctor's message in 1969, and were still killing Silents off-camera every once in a while. Or maybe the Doctor hadn't changed the timeline yet, so they were all under Silence control. Or maybe theory 4) below is right and the Silence hadn't changed the timeline yet so they weren't even on Earth in the timeline where we were watching Liz run around. None of those lead to any contradictions. The same options exist for Martha (except that in the first option there probably weren't too many left to kill).


 * River Song says that the child said that the Spaceman was going to eat her. The only way she could have heard this was through the phone of the President or recordings of these calls. However, it was the space suit which made the calls to the highest authority, so the girl would have to be already inside the suit when the calls were made.
 * I'm confused by what you're trying to point out as a plot hole here. One assumes once the President accepts the Doctors help, he is made privvy to the full extent of the phone calls and thus the Doctor tells his team what's on the tapes (River included.) Also, yes, the child is the space suit when the calls are made. So, what are you trying to say is the plot hole?
 * The only way that the message that the Spaceman is going to eat her could be sent, would be to be inside the suit itself. Therefore, the Spaceman has already ate her. So why would she say that the Spaceman is going to eat her?
 * The suit can connect to the president's phone line, no matter where he is. Starting a call from a phone in the same room would be fairly easy in comparison. Also keep in mind that the suit was there to protect the little girl. It mightn't be able to give her oxygen or stop her from needing food while she's outside of it, but surely it can make a phone call for her.


 * why didn't the soldiers question Nixon walking out of a large impregnable box that had been closed for days? surely they would have suspected some sort of trick?
 * Nixon is the President of the United States. They are not going to question him.
 * Keep in mind that these aren't just soldiers, these are soldiers who have been rewarded with one of the best assignments in the army (especially when the alternative was the jungles of Vietnam), and who are cleared for the highest levels of secrecy, so they're not likely to be the type that talks back to superiors. Also, in 1969, many soldiers were still enthusiastically pro-Nixon, and their first reaction would be, "Wow, I got to meet the President in person!" rather than, "How did Tricky Dick get in there?" And finally, I'm pretty sure soldiers stationed at Area 51 saw all kinds of bizarre things regularly, and were reminded on a daily basis, "It's not your job to think about it, it's your job to follow orders."


 * Amy was (presumably) captured by the Silents and the space suit after having marked tally counts on her arms and face. When she awakens in the pseudo-TARDIS control room, she has no marks. It's clear that the implanted recorder was taken from her hand; why do the Silents also wash her face and arms? Or do we catch up with a later version of her having missed a longer series of events?
 * The Silence could have washed the tally marks off so that Amy would not remember how many she saw at the orphanage.


 * How did River manage to shoot the last Silent without looking at it? Shouldn't she have been completely unaware of its presence?
 * She could have heard the Silence, or if she saw a dead Silence on the floor, she would still remember them.


 * Dwarf star material is not the densest or heaviest material in the universe. Even if black holes can't be used in construction, and quark matter (and preon matter, string matter, etc.) doesn't exist in the Whoniverse (we don't know whether it exists in ours), there's still neutronium, which we've actually seen used on the show. Given that human scientists had conjectured about neutronium years before 1969, and discovered actual neutron stars in 1967, and science fiction had been using it for years, the Doctor can't be lying to trick the humans or to avoid questions.
 * The Doctor says something like "a lot more happened in 1969 than anyone remembers" at the start of the whole thing. Does that mean that _he_ remembered it the whole time? If so, how? If not, what else could it mean?
 * If the Silence were running the show "since the wheel and the fire", why didn't they do anything about all those invasions and other crises in the intervening millennia? I can think of a few answers, but none of them are fully satisfying.
 * 1) The Silence assumed that Earth would be a reasonably safe place to conquer. They got very unlucky when Earth turned out to be the favorite place in the neighborhood to shake a conquering stick at, and just as lucky that the Doctor (and Sarah Jane, Torchwood, and a few others) always just managed to thwart the invaders and save silencity as well as humanity. That works, but it's kind of dramatically sterile to triumph over such a race.
 * 2) The Silence will have time travel in the future (which is how there was one at the picnic in 2001), and therefore they knew that the Doctor would avert these invasions. There may have been plenty of other invasions that they had to take care of themselves (or nudge humanity into taking care of), which we never saw because we're watching Doctor Who rather than The Silence Chronicles, or maybe there weren't. Possible, but how did they know that without also knowing that the Doctor would overthrow them in 1969?
 * 3) The Silence _have_ been doing something about it--they've been manipulating Sarah Jane, Torchwood, even the Doctor, and even in one instance the Master into saving the world all those times. That kind of takes away the whole point of the entire series; all those times we've watched the Doctor beat the aliens, he's just been the pawn of the Silence, saving humanity to continue being unwitting slaves?
 * 4) The Silence have been there since the wheel and the fire. But, until The Big Bang, they _hadn't_ been there since the wheel and the fire. Forgive the lack of time-travel-appropriate tenses here. Rory as we first met him had never been an Auton, but Rory a year later now has been an Auton, because time was rewritten. And time was rewritten in a big way--it was completely rebooted from the memories of the TARDIS crew and a bit of air from London in 2011. In fact, that may have been their entire plan last season. They set up the TARDIS explosion, knowing that the Doctor would come up with some clever way to avert it by making use of Amy's memories. They also insinuated themselves into Amy's subconscious memories. So, when history was recreated, they were written into it, going back thousands of years. Of course Amy, the Doctor, and the viewers all remember the old timeline, where the Silence weren't in control, and the Doctor was saving Earth for humanity. But The Big Bang created a new timeline, where the exact same actions by the Doctor were actually saving the Earth for the Silence. And, because the Silence had been present in the old-timeline 2011, they knew that their planet was safe at least until 2011. If I had to put money on it, this is the one I'd bet on. But I have a hard time imagining that the Moff would expect everyone to figure all this out, so unless they're planning on explaining it at great length in a later episode, there must be something simpler.