Doctor Who: Series 5 and 6: An Analysis of -REDACTED- (spoilers up through 6x03)
Disclaimer: First off, this post contains spoilers for Doctor Who series 5 and 6 (up to the currently aired episode, 6x03). Secondly, this post contains no spoilers for Doctor Who past season 6, episode 3. Please keep it that way in the comments.
So this is going to be long *puts on thinky thinking cap from Thinktown, Thinkania*
This is an analysis of the, hmm, main villain(s), lets say, of Series 5 and 6 of Doctor Who. I'm not even properly naming it/he/she/them outside the cut or in the title of this post so as to not spoil unsuspecting readers of this post.
So for the spoiler free, call this post "An Analysis of the Main Villain(s) of Doctor Who in Series 5 and in Series 6 (so far), With Particular Emphasis on Their Abilities, Various Foreshadowing in Certain Episodes, and Possible Appearances and Influences in Series 5."
Or for those who have seen up through season 6, episode two, the proper title is...
An Analysis of the Silence in Doctor Who
Part I: Concerning the Memory Erasing Effect of the Silence
There are several possible ways the mechanics of this works:
1.) The affected person's memory is completely deleted, starting from the moment that the Silence is first observed, and ending at the moment the Silence ceases to be observed, with the end and beginning being sort of pasted together. Using Amy's meeting of the Silence in the White House restroom as an example, Amy walks into the bathroom and a second later she finds herself walking out of the bathroom. If asked, she could not tell you one thing about what lay beyond the door to the ladies room.
2.) The memories are not necessarily erased, but have a sort of mental perception filter on them. e.g. Amy remembers everything that happens in the ladies room, but actively ignores the memory as unimportant. The mind's consciousness slides over the memory in the same way a person's eyes slide right over a visual perception filter.
3.) The memories are selectively edited to remove the Silence, and only the Silence. e.g. If asked, Amy could give a brief description of the ladies room she just walked out of, and might even be able to remember Joy, and give a brief description of her. She just wouldn't be able to remember the Silence, anything the Silence did, or anything she did as a result of observing the Silence.
4.) The memories are not deleted, merely blocked, according to the rules of #1, and become unblocked the moment the Silence is being observed again.
5.) A wibbly wobbly combination of all of the above.
I'm going with #5, as there are problems with each individual affect.
With #1, the main problem is that if someone starts to walk into a room, and suddenly finds themselves walking out of that room, that person notices. Amy would have noticed and freaked out instead of just looking at her phone in her hand and shrugging. Furthermore, we're talking about memory here. It's not like a piece of paper in a file cabinet. It's neurons and electro-chemical signals and all sorts of complicated things I'm not qualified to talk about. There are, however, clues to how the Silence work in certain scenes in episodes TIA and DofM.
In The Impossible Astronaut the basic rules were set up.
(1.)The moment you turn you back, you forget about the Silence. But it takes a second or two to fully kick in.
(2.) You remember past interactions with the Silence while you are observing one of them. e.g. Amy, in the restroom, remembering seeing the Silence at the lake and outside the Oval office.
(3.a.) You don't notice forgetting and anything out of the ordinary is shrugged off. e.g. Amy holding her phone and not knowing why she's holding her phone and not caring that she doesn't know why she's holding her phone.
OR
(3.b.) Your mind sort of "fills in" the gaps in your memory with fake, vague reasons for anything out of the ordinary e.g. Amy holding her phone and "remembering" that she pulled it out to check the time or something, but it wasn't important.
In Day of the Moon we learned:
(4.) You can remember making plans or deciding to do something that you thought of while observing the Silence, but this is not clear memory. It's more of a feeling that you're supposed to be doing something, a vague inclination without rhyme or reason. e.g. Amy "remembering" she's supposed to tell the Doctor something, but not knowing what or why. e.g. Canton fixing the Doctor's bow tie. e.g. the whole "plan" that was concocted between the end of episode 1 and the start of episode 2, but which we, the viewers, never saw, and which the Doctor and co. don't remember making.
And along with the basic rules, there were a few hints. In Day of the Moon when the Doctor has just reunited with the gang and he's talking to Canton, they have this exchange:
The Doctor: "... You keep checking your hand. If you've had an encounter, that's the first you'll know about it."
Canton: "Why didn't you tell me this before we started?"
The Doctor: "Well, I did, but even information about these creatures erases itself over time. I couldn't refresh it because I couldn't talk to you."
And then right after that, Canton casually looks to his side, then looks back at the Doctor and calmly adjusts his bow tie, or at least, that's the way it appears to Canton.
This one scene, I think, is the most important in defining how the Silence work.
As I said earlier, erasing memory isn't like pulling out a file and shredding it. I think the way the Silence work is more like trying to erase a wine stain in a white table cloth. The first go around, you can get most of it out, but there's still that pale purple stain. The second go around, it's even paler. You keep at it long enough, you keep bleaching it over and over, and eventually it will be completely gone, or as good as. But the tablecloth will be damaged, that portion of the cloth will be worn and frayed from the bleaching, maybe even have holes in it. But a few minutes of memory out of a whole lifetime is relatively small in comparison, so the damage from a few sightings is insignificant: a few square inches in miles of tablecloth.
However, if someone views the Silence while a previous viewing of the Silence is relatively recent, e.g. Amy seeing the Silence in the ladies room less than a day after seeing one at the lake and less than an hour after seeing one in the Oval Office., it's as if the original stain hasn't been completely bleached out yet, so not only is there a new wine stain on the table cloth, but wine gets re-poured onto the old spots, and the person gets all their recent Silence-related memories back, so Amy remembers the Lake and the Oval Office after a few seconds.
Of course over time, after too many viewings of the silence, the bleached spots become holes, and the fabric of the mind is tattered and worn beyond repair, e.g. the caretaker at the orphanage:
Amy: "... There's just one guy here, and I think he's lost it."
The Doctor: "Repeated memory wipes fry your head eventually."
So yes, I've done the stained cloth analogy to death, but the point is this:
A person gets their memories of previous Silence sightings back when viewing the Silence if and only if one of two things is true. (1.) The previous sighting is within a short enough time frame that the memory of the previous sighting hasn't been completely erased yet. In other words, the bleaching job isn't quite done. Or (2.) The person is reminded about the previous sighting within a short enough time frame. And this carries on, in that if someone is constantly reminded of what's going on, say via marks on one's arms, then even though they aren't actually viewing the Silence, they are sort of fighting back against the memory erasure, constantly strengthening the stains and resisting the mental bleach. So when the Doctor says:
The Doctor: "Well, I did, but even information about these creatures erases itself over time. I couldn't refresh it because I couldn't talk to you."
This one line opens up a whole world of possibilities for future plot lines as well as the ability to retcon any and all previous seasons.
1.) Concerning the retcon of the past. Basically, yes, it's entirely plausible. If Amy, Rory, River, the Doctor, etc. ran across the Silence in season 5, even if they ran across them several times in quick succession and so had memories of forgetting them, as long as they didn't write down the encounters or make some sort of record of them, i.e. "refreshed" their memories, they would have eventually been completely erased. So theoretically Amy could have seen the Silence hundreds of times before The Impossible Astronaut, but if it was long enough ago, she wouldn't have been able to remember any of those encounters at the lake or in the Oval Office or in the ladies room. The same thing goes for the Doctor and River. They might think Earth, 1969 is the first real time they've fought the Silence, but it could the seventeenth for all they know.
And so the whole of series five could be the events of series five as they are remembered but not be what actually happened. For example, in The Lodger the Doctor remembers the spaceship being empty and run by a computer program. Maybe it was. And maybe it was full of Silence. Amy, Rory, River and the Doctor all have no memory of the Silence being at Stonehenge during the opening of the Pandorica. Doesn't mean they weren't there.
2.) Concerning future interactions. By the time we get to some future episode in season 6, it's entirely possible that enough time has passed that Amy and Rory have completely forgotten 1969. Sure, at first they'd think about the Silence, and maybe have nightmares about being on the run, but without "refreshing" the information, over time, more and more would be erased, and the erasure would get more and more thorough and eventually that whole time period might just be a big gap that they'd never notice. And they really wouldn't notice after enough time elapsed. For example, if I asked you to remember one thing that happened yesterday, you'd be able to come up with something. If I asked you to remember one thing that happened on this day last year... well you wouldn't be alarmed if you couldn't come up with something. So eventually Amy and Rory will remember the blue envelopes and meeting up with the Doctor in Utah and the future Doctor's death and then going to rescue some pirates, but Canton and the future Doctor telling them to go to space in 1969, and maybe even the astronaut will eventually be forgotten.
I specifically mention Amy and Rory and not the Doctor, because I think the Doctor would keep "refreshing" his memory, unless...
3.) Concerning the crazy making properties of the the Silence's memory wipes
It's possible that the Doctor can't allow himself to refresh memories of the silence and remember them if doing so will eventually fry his brain. No one knows enough about Time Lord brains vs. human ones to say one way or another, but it's possible that he'll have to allow himself to forget. This harks back to my earlier point about this being the nth time the Doctor's fought the Silence, but being unable to remember it.
That's about it for the Memory portion of this Analysis.
Part II: On the Goals and Motivations of the Silence
It's a bit early in the game to really tell. We know from The Lodger that they're capable of hijacking the Tardis. From The Pandorica Opens and The Big Bang it's assumed, but not completely confirmed, that the Silence were the ones who hijacked the Tardis and blew it up. Whether they intended for this to destroy the universe, or if that was a giant "Oops. We just wanted to destroy the Tardis. Maybe a solar system or two in the immediate vicinity. Not everything." So that's still up in the air. We know they act parasitically, living off human civilization, directing it to achieve the goals they want. We know they've been on Earth for thousands of years before 1969.
However, there's a great deal more that we don't know about the Silence. Where do they come from? Why are they living on Earth? Why did they choose to direct human civilization and conquer the way they do? Are they doing this on other worlds? In other times? If so, when, where? If not, why Earth? What's with the spacesuit? The little girl? Amy? What happened to Rory at the end of TIA and how is he (and River) still alive at the start of DotM (Or are they still alive)? For that matter what happened to "Joy" in the ladies room of the White House. Yes, it looked like she exploded into ash, but in Doctor who that means nothing. If they have technology (in The Lodger) that can hijack a Tardis, what are they doing living in the sewers of Earth and why did they need Apollo tech? Why did they blow up the Tardis?
At this point, there's too many unanswered questions to do a full analysis, however, I do have a theory based on previous plotlines.
Part III: Concerning Foreshadowing & My Prediction for Series 6
Plotline 1) Things happening in the wrong order. e.g. River Song and the Doctor being "Back to Front" in their timelines. I think everyone can agree that Moffet likes his timey wimeyness. In series 5 there was a lot more of things happening because they happened than in the Davies era. Like Amy leaving the note in The Lodger after the crisis was solved. And in the Big Bang, Rory being able to get the Doctor out of the Pandorica because Rory had gotten the Doctor out of the Pandorica and the Doctor had then given Rory his screwdriver and told him to get the Doctor out of the Pandorica, etc. The whole idea of stable time loops (thing 1 causes thing 2 causes thing 3 causes thing 1) seems to be a favorite of Moffet's.
Plotline 2) "It's bad! No, it's good. Oops." While most see The Curse of the Black Spot as a standard stand-alone episode, I think it might be the most important for foreshadowing. We know from last season that there isn't such a thing as a throw away episode or plot line. The Beast Below: Forgetting things. The Time of Angels / Flesh and Stone: Don't look away. Don't stop observing. Vincent and the Doctor: Fighting an enemy you can't see. And the twist, that enemy itself being blind and afraid and only lashing out. The Lodger: Our first introduction to Silence tech and what it can do to the Tardis. Several of these could be considered stand alone episodes, not crucial to the central plot of the cracks in the universe, but they all foreshadow the silence.
Plotline 3.) The Doctor commits genocide. There's the Time War, obviously. Then there's The Vampires of Venice and the Sister of the Water asking the Doctor to remember her and her race before she jumps into the water to be eaten by her progeny. More series 5 foreshadowing
I think if you take the idea of a stable loop and combine it with the idea of a monster not being what it appears to be, you get the following.
We know humans expand out into the galaxy, breeding like rabbits, and "dancing" with every other species they encounter (if Captain Jack is anything to go by), and building empires and civilizations far and wide. And some point in this future, they encounter the Silence. They then begin a systematic extermination of them for no apparent reason. The Silence can't run. Wherever they go, they encounter humans, and humans always react violently to them, no matter what. They eventually figure out that the human race has been somehow conditioned to kill them on sight, but they don't know how or why. Their civilization is wiped out, but a small band of refugees manages to survive and escape to Earth's past where they begin careful observation and control of human civilization in an attempt to undo their own destruction. They watch and wait and carefully intervene here and there waiting for the event/thing that conditions the human race in the hopes of stopping it. In comes the Doctor and his Apollo 11 transmission.
So the Doctor becomes enemy #1, and the Silence do everything in their power to stop him / kill him / imprison him before he can get to 1969 in his own personal timeline. Hence, blowing up the Tardis in 2010. Which would mean series 5 happened after series 6 for the Silence. Moon Landing --> Human Conditioning --> Extermination of the Silence --> The Silence interfering in human civilization --> Moon Landing
A stable loop.
The 1103 year old Doctor, by this time in his life, knows what he's done. He can't undo it because that will create a paradox and destroy the universe. The loop has to happen. So he sends Rory and Amy and River on their way, knowing it will cause the genocide of the Silence. Which is why in TIA he looks so sad and regretful. He knows he's about to die, but he goes willingly because he believes he deserves it. It's his penance.
That's my theory anyway. I don't think it's going to be exactly that, obviously. It'll probably end up being way off the mark. My theory doesn't say anything about the Little Girl, the Astronaut, the Maybe-Could-Be Pregnancy, the Eye-Patch Lady, or a host of other things, but the general idea of the Silence not being the bad guys they seem and the Doctor being stuck in a loop that starts with him going to 1969 without knowing why and ends with him willingly going to his death in 2011 is the main idea.
Anyway, that's my two cents (*looks up* more like a buck and some change) on the first two episodes (well, technically three) of season 6. Any thoughts?
So this is going to be long *puts on thinky thinking cap from Thinktown, Thinkania*
This is an analysis of the, hmm, main villain(s), lets say, of Series 5 and 6 of Doctor Who. I'm not even properly naming it/he/she/them outside the cut or in the title of this post so as to not spoil unsuspecting readers of this post.
So for the spoiler free, call this post "An Analysis of the Main Villain(s) of Doctor Who in Series 5 and in Series 6 (so far), With Particular Emphasis on Their Abilities, Various Foreshadowing in Certain Episodes, and Possible Appearances and Influences in Series 5."
Or for those who have seen up through season 6, episode two, the proper title is...
An Analysis of the Silence in Doctor Who
Part I: Concerning the Memory Erasing Effect of the Silence
There are several possible ways the mechanics of this works:
1.) The affected person's memory is completely deleted, starting from the moment that the Silence is first observed, and ending at the moment the Silence ceases to be observed, with the end and beginning being sort of pasted together. Using Amy's meeting of the Silence in the White House restroom as an example, Amy walks into the bathroom and a second later she finds herself walking out of the bathroom. If asked, she could not tell you one thing about what lay beyond the door to the ladies room.
2.) The memories are not necessarily erased, but have a sort of mental perception filter on them. e.g. Amy remembers everything that happens in the ladies room, but actively ignores the memory as unimportant. The mind's consciousness slides over the memory in the same way a person's eyes slide right over a visual perception filter.
3.) The memories are selectively edited to remove the Silence, and only the Silence. e.g. If asked, Amy could give a brief description of the ladies room she just walked out of, and might even be able to remember Joy, and give a brief description of her. She just wouldn't be able to remember the Silence, anything the Silence did, or anything she did as a result of observing the Silence.
4.) The memories are not deleted, merely blocked, according to the rules of #1, and become unblocked the moment the Silence is being observed again.
5.) A wibbly wobbly combination of all of the above.
I'm going with #5, as there are problems with each individual affect.
With #1, the main problem is that if someone starts to walk into a room, and suddenly finds themselves walking out of that room, that person notices. Amy would have noticed and freaked out instead of just looking at her phone in her hand and shrugging. Furthermore, we're talking about memory here. It's not like a piece of paper in a file cabinet. It's neurons and electro-chemical signals and all sorts of complicated things I'm not qualified to talk about. There are, however, clues to how the Silence work in certain scenes in episodes TIA and DofM.
In The Impossible Astronaut the basic rules were set up.
(1.)The moment you turn you back, you forget about the Silence. But it takes a second or two to fully kick in.
(2.) You remember past interactions with the Silence while you are observing one of them. e.g. Amy, in the restroom, remembering seeing the Silence at the lake and outside the Oval office.
(3.a.) You don't notice forgetting and anything out of the ordinary is shrugged off. e.g. Amy holding her phone and not knowing why she's holding her phone and not caring that she doesn't know why she's holding her phone.
OR
(3.b.) Your mind sort of "fills in" the gaps in your memory with fake, vague reasons for anything out of the ordinary e.g. Amy holding her phone and "remembering" that she pulled it out to check the time or something, but it wasn't important.
In Day of the Moon we learned:
(4.) You can remember making plans or deciding to do something that you thought of while observing the Silence, but this is not clear memory. It's more of a feeling that you're supposed to be doing something, a vague inclination without rhyme or reason. e.g. Amy "remembering" she's supposed to tell the Doctor something, but not knowing what or why. e.g. Canton fixing the Doctor's bow tie. e.g. the whole "plan" that was concocted between the end of episode 1 and the start of episode 2, but which we, the viewers, never saw, and which the Doctor and co. don't remember making.
And along with the basic rules, there were a few hints. In Day of the Moon when the Doctor has just reunited with the gang and he's talking to Canton, they have this exchange:
The Doctor: "... You keep checking your hand. If you've had an encounter, that's the first you'll know about it."
Canton: "Why didn't you tell me this before we started?"
The Doctor: "Well, I did, but even information about these creatures erases itself over time. I couldn't refresh it because I couldn't talk to you."
And then right after that, Canton casually looks to his side, then looks back at the Doctor and calmly adjusts his bow tie, or at least, that's the way it appears to Canton.
This one scene, I think, is the most important in defining how the Silence work.
As I said earlier, erasing memory isn't like pulling out a file and shredding it. I think the way the Silence work is more like trying to erase a wine stain in a white table cloth. The first go around, you can get most of it out, but there's still that pale purple stain. The second go around, it's even paler. You keep at it long enough, you keep bleaching it over and over, and eventually it will be completely gone, or as good as. But the tablecloth will be damaged, that portion of the cloth will be worn and frayed from the bleaching, maybe even have holes in it. But a few minutes of memory out of a whole lifetime is relatively small in comparison, so the damage from a few sightings is insignificant: a few square inches in miles of tablecloth.
However, if someone views the Silence while a previous viewing of the Silence is relatively recent, e.g. Amy seeing the Silence in the ladies room less than a day after seeing one at the lake and less than an hour after seeing one in the Oval Office., it's as if the original stain hasn't been completely bleached out yet, so not only is there a new wine stain on the table cloth, but wine gets re-poured onto the old spots, and the person gets all their recent Silence-related memories back, so Amy remembers the Lake and the Oval Office after a few seconds.
Of course over time, after too many viewings of the silence, the bleached spots become holes, and the fabric of the mind is tattered and worn beyond repair, e.g. the caretaker at the orphanage:
Amy: "... There's just one guy here, and I think he's lost it."
The Doctor: "Repeated memory wipes fry your head eventually."
So yes, I've done the stained cloth analogy to death, but the point is this:
A person gets their memories of previous Silence sightings back when viewing the Silence if and only if one of two things is true. (1.) The previous sighting is within a short enough time frame that the memory of the previous sighting hasn't been completely erased yet. In other words, the bleaching job isn't quite done. Or (2.) The person is reminded about the previous sighting within a short enough time frame. And this carries on, in that if someone is constantly reminded of what's going on, say via marks on one's arms, then even though they aren't actually viewing the Silence, they are sort of fighting back against the memory erasure, constantly strengthening the stains and resisting the mental bleach. So when the Doctor says:
The Doctor: "Well, I did, but even information about these creatures erases itself over time. I couldn't refresh it because I couldn't talk to you."
This one line opens up a whole world of possibilities for future plot lines as well as the ability to retcon any and all previous seasons.
1.) Concerning the retcon of the past. Basically, yes, it's entirely plausible. If Amy, Rory, River, the Doctor, etc. ran across the Silence in season 5, even if they ran across them several times in quick succession and so had memories of forgetting them, as long as they didn't write down the encounters or make some sort of record of them, i.e. "refreshed" their memories, they would have eventually been completely erased. So theoretically Amy could have seen the Silence hundreds of times before The Impossible Astronaut, but if it was long enough ago, she wouldn't have been able to remember any of those encounters at the lake or in the Oval Office or in the ladies room. The same thing goes for the Doctor and River. They might think Earth, 1969 is the first real time they've fought the Silence, but it could the seventeenth for all they know.
And so the whole of series five could be the events of series five as they are remembered but not be what actually happened. For example, in The Lodger the Doctor remembers the spaceship being empty and run by a computer program. Maybe it was. And maybe it was full of Silence. Amy, Rory, River and the Doctor all have no memory of the Silence being at Stonehenge during the opening of the Pandorica. Doesn't mean they weren't there.
2.) Concerning future interactions. By the time we get to some future episode in season 6, it's entirely possible that enough time has passed that Amy and Rory have completely forgotten 1969. Sure, at first they'd think about the Silence, and maybe have nightmares about being on the run, but without "refreshing" the information, over time, more and more would be erased, and the erasure would get more and more thorough and eventually that whole time period might just be a big gap that they'd never notice. And they really wouldn't notice after enough time elapsed. For example, if I asked you to remember one thing that happened yesterday, you'd be able to come up with something. If I asked you to remember one thing that happened on this day last year... well you wouldn't be alarmed if you couldn't come up with something. So eventually Amy and Rory will remember the blue envelopes and meeting up with the Doctor in Utah and the future Doctor's death and then going to rescue some pirates, but Canton and the future Doctor telling them to go to space in 1969, and maybe even the astronaut will eventually be forgotten.
I specifically mention Amy and Rory and not the Doctor, because I think the Doctor would keep "refreshing" his memory, unless...
3.) Concerning the crazy making properties of the the Silence's memory wipes
It's possible that the Doctor can't allow himself to refresh memories of the silence and remember them if doing so will eventually fry his brain. No one knows enough about Time Lord brains vs. human ones to say one way or another, but it's possible that he'll have to allow himself to forget. This harks back to my earlier point about this being the nth time the Doctor's fought the Silence, but being unable to remember it.
That's about it for the Memory portion of this Analysis.
Part II: On the Goals and Motivations of the Silence
It's a bit early in the game to really tell. We know from The Lodger that they're capable of hijacking the Tardis. From The Pandorica Opens and The Big Bang it's assumed, but not completely confirmed, that the Silence were the ones who hijacked the Tardis and blew it up. Whether they intended for this to destroy the universe, or if that was a giant "Oops. We just wanted to destroy the Tardis. Maybe a solar system or two in the immediate vicinity. Not everything." So that's still up in the air. We know they act parasitically, living off human civilization, directing it to achieve the goals they want. We know they've been on Earth for thousands of years before 1969.
However, there's a great deal more that we don't know about the Silence. Where do they come from? Why are they living on Earth? Why did they choose to direct human civilization and conquer the way they do? Are they doing this on other worlds? In other times? If so, when, where? If not, why Earth? What's with the spacesuit? The little girl? Amy? What happened to Rory at the end of TIA and how is he (and River) still alive at the start of DotM (Or are they still alive)? For that matter what happened to "Joy" in the ladies room of the White House. Yes, it looked like she exploded into ash, but in Doctor who that means nothing. If they have technology (in The Lodger) that can hijack a Tardis, what are they doing living in the sewers of Earth and why did they need Apollo tech? Why did they blow up the Tardis?
At this point, there's too many unanswered questions to do a full analysis, however, I do have a theory based on previous plotlines.
Part III: Concerning Foreshadowing & My Prediction for Series 6
Plotline 1) Things happening in the wrong order. e.g. River Song and the Doctor being "Back to Front" in their timelines. I think everyone can agree that Moffet likes his timey wimeyness. In series 5 there was a lot more of things happening because they happened than in the Davies era. Like Amy leaving the note in The Lodger after the crisis was solved. And in the Big Bang, Rory being able to get the Doctor out of the Pandorica because Rory had gotten the Doctor out of the Pandorica and the Doctor had then given Rory his screwdriver and told him to get the Doctor out of the Pandorica, etc. The whole idea of stable time loops (thing 1 causes thing 2 causes thing 3 causes thing 1) seems to be a favorite of Moffet's.
Plotline 2) "It's bad! No, it's good. Oops." While most see The Curse of the Black Spot as a standard stand-alone episode, I think it might be the most important for foreshadowing. We know from last season that there isn't such a thing as a throw away episode or plot line. The Beast Below: Forgetting things. The Time of Angels / Flesh and Stone: Don't look away. Don't stop observing. Vincent and the Doctor: Fighting an enemy you can't see. And the twist, that enemy itself being blind and afraid and only lashing out. The Lodger: Our first introduction to Silence tech and what it can do to the Tardis. Several of these could be considered stand alone episodes, not crucial to the central plot of the cracks in the universe, but they all foreshadow the silence.
Plotline 3.) The Doctor commits genocide. There's the Time War, obviously. Then there's The Vampires of Venice and the Sister of the Water asking the Doctor to remember her and her race before she jumps into the water to be eaten by her progeny. More series 5 foreshadowing
I think if you take the idea of a stable loop and combine it with the idea of a monster not being what it appears to be, you get the following.
We know humans expand out into the galaxy, breeding like rabbits, and "dancing" with every other species they encounter (if Captain Jack is anything to go by), and building empires and civilizations far and wide. And some point in this future, they encounter the Silence. They then begin a systematic extermination of them for no apparent reason. The Silence can't run. Wherever they go, they encounter humans, and humans always react violently to them, no matter what. They eventually figure out that the human race has been somehow conditioned to kill them on sight, but they don't know how or why. Their civilization is wiped out, but a small band of refugees manages to survive and escape to Earth's past where they begin careful observation and control of human civilization in an attempt to undo their own destruction. They watch and wait and carefully intervene here and there waiting for the event/thing that conditions the human race in the hopes of stopping it. In comes the Doctor and his Apollo 11 transmission.
So the Doctor becomes enemy #1, and the Silence do everything in their power to stop him / kill him / imprison him before he can get to 1969 in his own personal timeline. Hence, blowing up the Tardis in 2010. Which would mean series 5 happened after series 6 for the Silence. Moon Landing --> Human Conditioning --> Extermination of the Silence --> The Silence interfering in human civilization --> Moon Landing
A stable loop.
The 1103 year old Doctor, by this time in his life, knows what he's done. He can't undo it because that will create a paradox and destroy the universe. The loop has to happen. So he sends Rory and Amy and River on their way, knowing it will cause the genocide of the Silence. Which is why in TIA he looks so sad and regretful. He knows he's about to die, but he goes willingly because he believes he deserves it. It's his penance.
That's my theory anyway. I don't think it's going to be exactly that, obviously. It'll probably end up being way off the mark. My theory doesn't say anything about the Little Girl, the Astronaut, the Maybe-Could-Be Pregnancy, the Eye-Patch Lady, or a host of other things, but the general idea of the Silence not being the bad guys they seem and the Doctor being stuck in a loop that starts with him going to 1969 without knowing why and ends with him willingly going to his death in 2011 is the main idea.
Anyway, that's my two cents (*looks up* more like a buck and some change) on the first two episodes (well, technically three) of season 6. Any thoughts?