WARNING! THERE MAY BE UNMARKED SPOILERS!
Flesh (from The Rebel Flesh) is based upon Vespene tech.Because I recall that The Doctor mentioned there being alien technology involved in the process, and the process seems to be akin to that of the Vespene duplicates. It also would explain Rory's empathy, as he remembers being a Vespene duplicate.
The "flesh" technology from The Rebel Flesh is related to Sontaran cloning technology.The Doctor mentions it's somehow alien in origin and in a season four two-parter (Doctor and Donna travel to earth to answer a distress call from Martha Jones) the Sontarans clone a copy of Martha in a similar looking vat. Also, the brass-looking acid suits are very similar in shape to the general Sontaran suit shape. Rebel Flesh cloning technology is either derived from Sontaran tech or is actually the origin of Sontaran technology. And to be honest, even if this is Jossed, it would have still worked really well as a plot.
The Flesh is related to the technology used on Gallifrey to create new Time LordsThe Doctor was too freaked out by that goop for it to not have some greater relevance, and he was rather reticent to discuss it. It hasn't just made a copy of the Doctor, it's made a completely functioning Time Lord, with all the regenerative and superhuman powers that would suggest, as well as implying that the Time Lords are (of course) not completely done for.
Possible motives for the Doctor's allies in A Good Man Goes To War.
Madame Kovarian has personal reasons for trying to kill the DoctorIt just feels that way. She risked her life for this plan to work but still said the Doctor is a good man (and good men have rules). She hasn't been foiled by the Doctor many times before (in his timeline), so we can assume it's in her future. Adding to that, the reason she didn't just shoot the Doctor or set Demons Run to explode (making sure that she's the only flesh copy left and thus eliminating anything Time Lord-like) is that something he did in his future made all this possible, or gave her her motivation in the first place. The trap is to send him to either find a younger Kovarian and give her that motivation or make all this possible in some other way.
Madame Kovarian is a female regeneration of the Master.It would explain her obsession with him; maybe the Master went crazy/crazier after John Simm's version regenerated into Frances Barber's version and decided on killing the Doctor instead of flirting with him. She certainly does act a little like the Master's Large Ham self in Closing Time, and the Master's being "a bit hypnotic" could explain how she got the clerics and the Silence on her side. Finally, all that Tick-tock stuff has got to be related to the drumming somehow.
The company in The Rebel Flesh works for the Sontaran EmpireThink about this for a moment: Sontarans reproduce exclusively via cloning, they cloned Martha Jones in a manner very similar to The Flesh, and those Anti-Acid suits look an awful lot like a Sontaran Battle-Suit...
Series Six will deconstruct Davies' habit of not knowing when to quit with his pet characters by having River turn out to be Not A Nice Person, Period, or perhaps just an especially persistent admirer of the Doctor's.The Doctor will eventually have to reboot the Randomiser just so she'll go away and people will stop talking about her, already.
Madame Kovarian is Amy's Valeyard.Much like how the Valeyard is the distilled, potential evil inside the Doctor's heart, Kovarian is the embittered possible future version of Amy Pond. Amy Pond is a Paradox Person who grew up with the cracks in time, so alt-timeline versions of her could easily exist. Said alt-future version? The bitter, Doctor-hating Amy Pond from "The Girl Who Waited." Kovarian decided to kidnap Melody Pond as a sort of twisted, degenerated take on her desire to raise the daughter she lost, combined with the Stable Time Loop of Amy's life. She looks different because Kovarian is trying to dissociate herself with her past self. Her being a Valeyard expy would foreshadow the appearance of the actual Valeyard
We will never get the answer to the First Question."Silence will/must fall when the Question is asked." Moffat is telling us that if we ever learned who the Doctor is, the show would Jump the Shark and eventually be cancelled, becoming "silent."
The first question - Doctor Who? - Death is the only answerMore precisly the doctors name and the answer to the first question is Death. Remember the Doctor who mini-episode in which the doctor meet Albert Einstein and Einstein turned into an Ood, well it was written by a group of children and was supposedly revised slightly by Moffat. The name of it was Doctor Who - Death Is the Only Answer. The question doctor who is asked and answered in the title and secondly the phrase appears in the episode but really do not make much sense in context and it feels a bit to morbid to have been written by a group of children. Doctors name is death.
We already know the Answer to the Question.It's 42, naturally.
The Question is "What is the Doctor's name?"
The First Question... is "Doctor who?"
River will be there, on the Fields of Trenzalore.That's when she learns his name, because he has to answer the Question.
The Answer is...
Eleven: "...well, I don't know."There's a good reason why the Doctor never tells anyone what his name is — even he doesn't know! It's been basically proven (both in canon and by Wordof God that he doesn't really know how old he is — in the classic series, he's been known to call himself over a thousand years old, but now he's in his nine hundreds. So, why/how would he really remember or know what his name is?
The Answer is...
The Doctor's name is 42.We always knew the answer. Now we know the Question. Just for heaven's sake don't answer the Question.
The Doctor's name is "The Doctor".Hear me out. What is a name, really, but a statement of who you are? His name is The Doctor because that is what he is, a healer, the man who makes people better, even, as they say in the gamma forests, a great warrior. The Doctor is his name because it is what he has become. Confirmed: That was the answer Clara gave and the Silence did fall...
The Twelfth Doctor will answer the Question.The Fall of the Eleventh, it could be the regeneration of the Eleventh Doctor. It has been widely theorized that the Tenth Doctor spent a regeneration on his hand, which would make the Twelfth Doctor the last. Who better to reveal his last remaining secret?
The Doctor will reveal the Answer because he's just plain given up on going on.The experience that leads up to his final regeneration may be so unpleasant and tiring that, having finally had enough with everything ever, he will just drop everything he's been clinging onto and essentially go, "Fuck it. You want to know? You really want to fucking know? FINE."
The power of the Answer is a side effect of the Doctor's greatest malady...Essentially being God. Through his actions, the Doctor has become the most important person ever to have lived. The one thing he holds sacrosanct above all others is his name, so it has become such on a universal level. When it is revealed, that's it. No more point in going on, for anyone or anything, even time and space themselves.
There is no Answer, and asking the Question will kill off the Silence, not the Universe."Silence must fall when the Question is asked", right? What I figure is that it's a Self-Fulfilling Prophecy / Petard-Hoisting about the end of the Silence themselves. They'll all end up at Trenzalore to prevent the Doctor from getting there (which will backfire spectacularly, natch), someone will ask the Question, and whatever's in charge of Trenzalore that prevents you from speaking falsly or refusing to answer will have some kind of massive freakout when faced with a question that doesn't have an answer. Boom go the Silence, boom goes Eleven, hello Twelve.
The Question's status as the First may have been the result of a particularly wibbly-wobbly Stable Time LoopIf the Question's immense power is derived from its status as the First... bear with me. When time broke down and the distress signal was sent, it was sent all across time... including the very beginning, when the very first sentient mind in the universe to be capable of understanding it, at the very beginning of its sentience, wouldn't have had a damn clue who the Doctor was. It's wibbly-wobbly because the universe hadn't contained that event yet when the Question's status became known and the Silence were formed and they tried to kill the Doctor with River Song. Of course, it's not really a time loop if the fact that it's the First Question isn't what makes it so dangerous.
The First Answer
The "Fall of the Eleventh" does not refer to the Eleventh Doctor's regeneration.Because that's just way too obvious. And too soon.
The question does not actually refer to his name, but that's how the Doctor will answer it anyways.Just because he has to tell the truth doesn't mean he can't "misunderstand" the question...
The Answer to The Question of "Doctor who?" will be a meta-reveal that it was a show all along.
Jesus is the Answer.
The Answer is...
We'll never hear the Doctor's real name.We know that his name is pronouncable by humans, and in a reasonably short amount of time, because River Song whispers it in his ear. The reason he doesn't tell other people is because, by extraordinary coincidence, his name sounds exactly like a string of English curse words. They simply can't air his name on TV, and the Doctor doesn't like to say because it sound's like he's just swearing for no reason at other people.
Companion: Doctor, what's your name?
Companion: Well, fuck you too! Jeez!
The Doctor's real name is "Victorious"Well actually the word that means 'victorious' in Galifryan, hence why he once said it was unpronouncable to humans.
The Question, asked in context, is "Doctor, who?"The question isn't being asked of The Doctor, but to The Doctor. Because the context changes everything.
The Answer will be "Valeyard".
Literal "silence" will fall.The most anticlimactic interpretation possible: when the question is asked, everybody will just shut up for a moment to hear the answer, ergo, silence will have fallen. Then the question will be answered and back to business.
The First Answer is......an anagram of the phrase 'the Medusa Cascade', or possibly just 'Medusa Cascade'. It's hidden in plain sight!
The Doctor will not answer the Question with his name...One, because there is no way to reveal it without basically ruining the greatest mystery in television history, and two, because he said so himself in "Asylum of the Daleks".
The answer is "I'm Batman"Not saying this seriously, but much like how we often can see that X is a Time Lord, there is sufficient evidence that the Time Lord's true name is, in fact, Batman.
Trenzalore is a point where realities and timelines intersect, a "Dark Tower"-esque hub of the universe.
The answer to the question will be, simply, "yes".On the Fields of Trenzalore, at the Fall of the Eleventh, when no living creature can speak falsely or fail to answer, a question will be asked. Knowing this, the Doctor will try to warn whoever he is with, at which point they might ask: "Which question? Doctor Who?"
Some double meaning to the exact words of the questionThe only time the question is explicitly quoted - at the end of The Wedding of River Song - Dorium repeats the words three times, placing particular emphasis on the final syllables "DOC - TOR - WHO". When the Doctor says it at the end of Asylum of the Daleks, he does so exactly the same way. The repetitions and also the pronunciation of the last bit could have particular significance.
The series will change name once the question is answeredIt will become "Doctor <actual name of the Doctor>". Hence all the ominous predictions about the end of the universe: it's the end of a series and the beginning of another. Granted, it's not likely to happen, but I really expect something very meta as far as this answer is concerned. Right now this is all I can think of.
The answer to the first question will be...
As suggested above, Silence Must Fall because the Doctor has no real name.As it turns out, the Doctor has been hiding from his name literally all his life-as in, from having a name in the first place. For whatever reason, the Doctor's parents/pre-incarnation/whoever refused to give him a name because of the power of a lack of a name. That, and possibly whatever's causing the time cracks could be held off with such a power. Now, I bet you're asking, if this is the case, how did River tell the Doctor his name? She didn't-she simply said that he was nameless. The Doctor wouldn't be able to say anything when truthfully answering "Doctor Who". There'd just be silence.
The eyepatches let people remember the Silence
The Silence and the Silents are two different things.The Silents are an alien race that serve something called the Silence or are working towards an event called the Silence. Thus when they say Silence will fall, they are not referring to themselves, rather to their goals.
The Silents and the Ood are closely related
Between 1969 and 2011, The Silence did something to reverse or counter the hidden extermination order in the moon landing.It is unlikely that Amy, Rory or River never saw the moon landing video during their lifetimes, but none of them were compelled to kill any Silent they see on sight. With those two episodes being a Stable Time Loop set up by the future Doctor (supposedly), they should have been affected but they weren't.
The Silence are behind the whole of Madame Kovarian's operation, and also the attempt to blow up the TARDIS (without knowing the consequences).The motivation for the anti-Doctor group led by Madame Kovarian still hasn't been adequately explained ('boo-hoo the docter is scary' doesn't quite satisfy me), and the idea of 'Silence will fall' was set up as being way too big to blow its whole load in the first two episodes (and we know that the characters from the Lodger will return...) so after the Doctor destroyed the Silent Empire, they created the Anti-Doctor organization slowly (only took 'em three millenia) as a means of revenge against him. This is actually plan B after plan A - blow up the TARDIS - somehow failed (I guess the voice in the TARDIS just before it explodes is a silence? Maybe).
The Silence are SlendermenOr their leader is. They look remarkably similar (Tall, Slender, Male, in a suit) and fans have wanted this for a while and Steven Moffat complied.
The Doctor has encountered the Silence before.However, he has (naturally) forgotten all about them. One of the Silence mentioned being on Earth since fire and the wheel. The making of fire was a major goal of the cavemen in the very first episode of the series. The Doctor wasn't all that heroic in this episode, so intentional thwarting is somewhat out of the question. Accidental stowaways on the TARDIS perhaps? Stranded in pre-history, their plans for recovery delayed by the Doctor, whether he knew it at the time or not.
The Silence aren't, as a whole, actually evil.Aside from traitors or others coerced in some way, they are more than content to share the Earth and help humanity (and themselves). Perhaps the Doctor was used to try and exterminate them once the Silence organization didn't need them anymore, which nearly succeeded. He will then free and help the enslaved ones, who will then go back into obscurity and live as they always did.
There's a Silent hiding within the TARDISAt two points in the Lodger, there are scenes where Amy, stuck in the TARDIS as it tries and fails to complete a materialisation, is talking to the Doctor when something odd happens. As the Doctor talks, once in Craig's spare room and once on the football field, Amy looks off screen, gasps and looks shocked and then cries "Hey!" before the scene carries on as usual. During the second time, as she reacts like this, the Doctor says "Hang on" as she cries "Hey!" - she repeats his "Hang on" in an uncertain tone of voice and shakes her head as if trying to wake from a tired state. Later on, as the Doctor and Craig race upstairs to help Sophie and Amy experiences turbulence in the TARDIS, over the earpiece she can be heard to cry "Doctor!", and then inexplicably say "Hang on..." in the same uncertain tone that she did earlier. Her actions here aren't explained. Perhaps the Silent was the pilot of the primitive TARDIS above Craig's flat, and the disturbance that caught the TARDIS was it managing to transport itself into the Doctor's TARDIS. On two occasions, Amy saw it darting away from her out of the room, causing the reaction, but the trademark effect of the Silence kicks in and she immediately forgets it happened. As we also know that seeing the Silence can leave a post-hypnotic suggestion in a person's mind, maybe seeing this Silent accidentally left the Doctor's command of "Hang on" in Amy's mind, which then came back to her mind when she was again in danger of being lost in the Vortex as the Doctor was warning her about. It's not long after this - the next episode, in fact - that the TARDIS inexplicably shoots off to 26/06/2010 with River Song and explodes despite her efforts - was the Silent in the TARDIS sabotaging it? And if it was, was it killed in the explosion, or could it have survived? Could it still be in the TARDIS even now, watching the Doctor? And if it is, what happens when it warns the rest of the Silence that the Doctor survived Lake Silencio?
The leader of the Silence is The Master.The cracks allowed for the Master to escape from the Time War. Then, using mind control and his knowledge of the Doctor, he formed the Silence, the "Silence" referring to him wanting to silence the drums in his head. The TARDIS exploded because of the master expoiting his knowledge of TARDIS's and possibly the laser screwdriver and it was blown up to cause a Stable Time Loop where the cracks appear because the TARDIS blew up allowing the master to escape in the first place. The Pandorica was built so that the Doctor would cause the Big Bang II and stop the universe from ending so that the Master could rule over it.
The Silence are the reason why The Grey exists.Think of how alien abductions go? You're kidnapped by immaculate humanoid figures with bulbous heads, big old eyes(or in the Silence's case, eye-sockets) and super-advanced technology. You can't directly remember it, its usually recalled via hypnosis and dreams and there's no physical evidence. Sounds like the Silence, doesn't it? While the abducted can't remember what happened, the Silence did enough so that the idea of "something" kidnapping them remains(or the Silence allowed a subconscious memory so that the idea of actual alien abduction is laughed off as a delusion). The Grey is an attempt to fill in the blanks-and long before we thought up of the idea of an alien, we thought they were demons, angels or even faeries. After the moon landing, the Silence had to deal with them while they were delirious or asleep, allowing them to restrain you before they can grab a weapon-hence why those abducted by aliens in sleep recall being paralysed during all this.
The Silents were not constantly manipulating humanityIf so shouldn't they have been in Berlin to interact in Let's Kill Hitler? I prefer to think that they do manipulate humanity but most of the time just a small number observe humanity. At certain points they again start to manipulate humanity, like when they really need something. If they were really constantly manipulating humanity it would probably soon have fallen into chaos without their manipulation. Perhaps the Silents started wide-scale interaction again around the Cuban Missile Crisis to prevent nuclear war, and continued to 1969.
The Silents influenced Xerxes to invade GreeceApparently Xerxes after his Uncle Artabanus told him not to invade Greece decided not to. However according to Herodotus a tall man appeared over his bed and told him to do so. This happened the next night and Xerxes told his Uncle the same thing would happen if Artabanus slept in his bed. Artabanus did so and the man threatened to burn Artabanus' eyes out. Thus Artabanus told Xerxes he should invade Greece. The man could have been a Silent, they wanted an invasion for some reason so influenced Xerxes, but he could slightly remember the Silent. Maybe they weren't as good at memory erasure during that time.
The Silents shut down [[Torchwood The Time Agency.]] Canon states the Time Agency ended around the 52nd century-the same time period that the Church of the Silence was around. I doubt the Silence wanted a group of opportunists threatening their plans.
The Doctor never told River his name
The Gangers are the origin of the ChangelingsNo noses, pale faces, born from (and reverting to) goop, able to switch between Ganger and human looks... Now they just need to get their own planet and cover the surface of it.
The Guardians are behind the events of seasons five and six.The two Guardians are playing a game of Xanatos Speed Chess with each other, and both are trying to manipulate the Doctor for their own purposes. However, as they caused the Time War (come on, something that big has those two written all over it), they can't let the Doctor know it's them, as he's understandably a bit upset with them. In the trailer, it said that Amy, River and Rory had been recruited, and we also have a shot of the Doctor imprisoned, which could be to do with them. This implies that:
The Silents are trying to save the universe.From what we've seen, the Silents aren't the cosmic retgonners we've been led to believe. I'm going out of a limb here, and not only saying their benevolent, but actively trying to stop the cracks. They are one of the many species who fear the Doctor, and see him as responsible for the cracks. They have allied with Korvarian, in a misguided attempt to stop the Doctor. The Doctor's genocide of their race is confirmation that they are in the right. Why are they so terrifying? Good Is Not Nice, of course. The Doctor must sort things out, unless the true villain becomes victorious.
The planet in The Doctor's Wife is Mogo.1. Sentient planet, that talks with a deep voice. 2. Inhabited by crazed derelicts, who turn out to be not very nice. 3. Green glow everywhere. Equals: The planet is Mogo.