These are updated notes with everything I know. If you have any information to add, let me know and I'll toss it in. I took out the references to the cracks except for in Episode 11 (where I list them all at once) because they have been repaired.
I am gonna go back and watch the episodes again one by one and I'll add stuff as I go, so make sure to check back and see if more has been added as the weeks go on.
Episode 1: Eleventh Hour
Starting 14 years ago would mean this episode starts in 1996, spends a lot of time in 2008, and ends in 2010.
Questions:
Prisoner Zero's species is never really determined. The Atraxi seem a lot like the Judoon in the way they handle escapees (who cares if everyone ELSE dies as long as the case is closed?) I doubt we've seen what the real Atraxi look like; I think they probably look very different and that was just their (bad pun coming here) “eye in the sky.”
Duck pond with no ducks?
The universe is cracked. Pandorica will open. Silence will fall. The Doctor certainly doesn't seem to know-or if he has he's forgotten.
We can neatly dismiss the first two statements as they have already occurred. The Universe has been cracked and put back together (but may be cracked again-keep reading.) The Pandorica has opened (and been blown up.) But silence, apparently, has yet to fall. In the promos for series 6, it's been titled as “The Silence.” Whether that's a state of being, a species, or some sort of fuzzout signal interference, I don't know.
Prisoner Zero also taunts the Doctor on his lack of knowledge about who opened the cracks in the first place. At this point I would assume it's either him or River, and their past selves then fix the problem.
How does the TARDIS key get into the Doctor's pocket?
One thing I did NOT spot and that someone else did is Rory's ID. Rory is Amy's boyfriend in 2008 and he's her fiance in 2010. They've grown up together-she's known him all her life in Leadworth.
BUT something is NOT right with Rory's nurse ID, issued from the hospital.
(Ta to alienpanda for the sharp eyes)NOTE THE DATE. 1990? We assume Rory is standing there 18 years later (in either 2007 or 2008.) Something is NOT right here. It's perfectly obvious to me (having had it pointed out) that there's more to Rory than meets the eye. And the Doctor knows more than he's letting on, since we only saw this ID in his mind's eye.
The head writer is a stickler for details-on the making of, the crew were placing postcards with the name of the town on them in card racks-so this isn't a mistake or a goof. The fact that the director focused on it for a long while in the Doctor's mind is another clue that this is terribly important.
Recall from watching this Doctor all 14 episodes so far that sometimes he sees things and misses it, and comes back around to it later and puts the pieces together. This might be one of those times.
Another thing that seems to bother some of the Who fans is the high amount of coma patients in the small town of Leadworth. They don't even have an airport-so why do they have at least 6 coma patients (may be more in the next room over that we couldn't see) in a HOSPITAL no less? Wouldn't they have all been moved to a long-term care facility? I don't know how many coma patients an average town should have but 6 seems a tad high.
Episode 2: Beast Below
How'd the Queen and her entourage know the Doctor was coming?
I thought Magpie got eaten by the Wire, so why is his business still around in the year 3295?
Episode 3: Victory of the Daleks
How did Amy not know about the Daleks?
The Doctor seemed very pissed at the Daleks here, and it seemed a little out of place. Certainly previous Doctors have treated them with distaste and loathing, but his wooden malleting of the Dalek in front of him was almost an overreaction. I wonder if he took a spin out in space before he went to see Amy the third time around in the first episode and ran into them, thereby setting him up to be angry here.
Or maybe I'm reading too much into it.
Episodes 4 and 5: Time of Angels/Flesh and Stone
River acts very much like a first-season Jack here (reckless, ruthless, a lot flirty) which makes me think she might be from the 51st century herself (could even be related to Jack.) Remember, we assume her name is River and we assume she's from the 51st century (a good bet, seeing as she has knowledge of future tech like Jack does.)
Who wrote the diary? Was it the creator of the Angels? Did his dreams get away from him and become the infinite evil that is a Weeping Angel? Will we ever meet the poor sucker that wrote the book?
There is probably a connection to Prisoner Zero here, boosted by this picture:

(thanks to the people over at digitalspy for the photo)
Is that an Atraxi looking over River's shoulder, watching her? Does River know Prisoner Zero? Were they in the Stormcage together? Did River help them escape?
We find out here that:
River can fly the TARDIS. She states here that she didn't learn from the Doctor, but later on in Episode 12 she will state that she did. She might not be lying either way; it's possible for a time traveler to have both events occur. So she might have not learned from him in one timeline but learned from him in another. It certainly would explain how she flies it so neatly compared to the way he does it, but the question remains: If she didn't learn it from him, WHO'D SHE LEARN IT FROM?
River knows Old High Gallifreyan. She has yet to say who she learned that from.
She has pictures of all his faces (wonder if she got the book from his human episodes or whether she went to UNIT or whether she nagged Jack for them?)
They are married but River states that it's more complicated than that. I assume Timelord marriages are deep and complex things that involve a linking of minds. It also would mean that she would know his real name, the one we don't know. Human marriage would seem very shallow by comparison.
She would have to be one special human for him to do the marriage thing with her. A human-Timelord marriage would most likely be a difficult thing for both as it's cross-species, and probably would not have existed if the Timelords were still around (unless we're sticking to the stupid theory that his mum or dad was human, which I don't.)
She killed someone (a good man, the best man she'd ever known) and was put into Stormcage for it. If the Doctor knew who she'd killed, he would most likely stop working with her at this point in his timeline. He hasn't experienced the incidents yet and when the events occur WILL understand what has happened and therefore accept whatever she does as all right.
What remains to be seen is who she killed and why. It's not probably the Doctor (too obvious) and she cares nothing for Rory at all (if she'd killed him she might have reacted a little bit more than she seems to have so far.)
The interesting thing about this is that those Church guys know she's a murderer. All of them do. Yet they follow her lead into the catacombs, no question. They seem to have no problem working with her and trusting her, despite knowing that she has done serious wrong.
I also wonder to myself WHY they let River keep her gun and hallucinogenic lipstick even when she was KNOWN to be a murderer? I can see her wearing the lipstick in, but she couldn't have gotten in a gun without them searching her.
My theories after these episodes were either that River was a spy for the Church or a researcher/archaeologist for the Church. I surmised that at some point in her life, she may have met and hung out with a Timelord who was allies with the Doctor at one point or another. My most likely theory was that she had met Romana, as she acts a hell of a lot like her sometimes.
I do NOT believe she is Time Lord in any portion (as he would have figured that out already) and I don't believe she's fobwatched because she'd have the ditzy thing going on because she couldn't remember who she really was (and River's not ditzy.)
It's also possible that she could have hooked up with Omega and may be working under his orders to get under the Doctor's skin. More on that when we arrive at Episodes 12 and 13.
Episode 6: Vampires in Venice
"In memory of the children lost to the silence..."
You could travel to other worlds through the cracks but they would snap shut behind you. Might be something to consider, since it hasn't happened to the Doctor yet and it probably will.
Rory acts oddly when he gets into the TARDIS. He says he's done research and seems to know quite a bit, but the blank stare throws me a little.
At the end of this episode, Rory hears silence but the Doctor hears a voice. Even after two runs over the spot I couldn't get WHAT was being said or WHO was shouting but that was definitely a voice. It might be the voice we hear at the end of the series.
Episode 7: Amy's Choice
Wonder if the aliens popping out of the old people were Atraxi relations, because they certainly looked familiar (indeed, if that's what the Atraxi look like.) According to Whowiki they are Eknodine and they DO exist in the Whoniverse because the Doctor knew who they were. These could be related to the Atraxi from episode 1.
And we find out at the end that it was all psychic pollen and made the Doctor make a Dreamlord and two false realities. Something about this just doesn't sit right-did he do this on purpose to drive Ames toward Rory? Because two episodes ago he SAID he was going to fix it and NOW he has. Hm. Convenient, no?
Once again, we see a possible manifestation of the Valeyard, or the "nasty charismatic world-smashing baddie that the Doctor is supposed to turn into around his 12th or 13th body and which he fears becoming." He showed a small hint of it with Ten in "Waters of Mars" when he decided he was in charge of time and space and could do as he pleased. It's the evil half of the Doctor, the demon with the face of an angel. He may look nice, but can manipulate and charm you into walking off a cliff or blowing up a planet. Hence, he's a lot frightening and not someone you want to let out.
Which would explain why when the Doctor saw him in the last seconds of this episode on the console of the TARDIS, he seemed afraid of him.
Episodes 8 and 9: Hungry Earth/Cold Blood
The Doctor calls for silence (significant?)
Clennparii (sp?) defense is the defense of oneself by saying you're the last of a species. The Doctor was more than moderately insulted when the Silurian in captivity dared to claim this defense, since at this moment he IS the last of the Time Lords. This might be important as the Doctor might have to use this as an out at some point along the line.
We're gonna skip over Episode 10: Vincent and the Doctor because while it was a great episode, there wasn't much that hasn't been explained about it.
Episode 11: The Lodger
This episode still bugs me, mostly because the whole plot rests on a TARDIS sitting UPSTAIRS sucking people into itself, trying to find a pilot and causing time loops every time it does. The Doctor's fairly nonchalant reaction was kind of wrong. It was a TARDIS, dammit. He should have been wondering who parked the thing THERE and WHY. Not just anyone could have parked it there (River? Omega?) He couldn't POSSIBLY have known it was up there, otherwise he would have just sent Sophie and Craig up there together and had the two of them fix it. He wouldn't let a bunch of innocents die just to satisfy his curiosity.
Since the guy who played Craig is coming back for another episode, it's a good bet that we're going to catch up with him and Sophie in Thailand with the monkeys and we might get a glimpse of who parked that damn TARDIS on the roof of Craig's old flat.
Cracks in the year 1580, 1941, 1996, two in 2010, 2020, 3295, and the 51st century.
Episodes 12 and 13: Pandorica Opens/Big Bang
The ship in space with everything headed towards it looked a lot like the one that just got vaporized last episode. Possibly the same one before it disappeared?
The Doctor mentions the Trickster and the Warrior. Tricksters have shown up a few times recently-there was the beetle on Donna's back in Series 4 and the whitefaced thing that tried to kill off Sarah Jane in her show. The Warrior could be the War Chief or Omega (if indeed it is a Time Lord we're facing here-and how could we not be with all these damn time cracks?)
Someone claims the loudspeakers in the ship and causes CRACKS across the SCREEN and says SILENCE WILL FALL and bloody hell, that sounds like Davros if I'm not mistaken.
Well, that was my first impression, and of course we have no earthly idea who the being behind the voice is, but here's a few theories...
Clearly it's a man, clearly an older man. Since Davros usually liked to show up and be in the middle of the riot he was causing and since we saw him at the end of Donna's time in the TARDIS I don't believe it's him. I would be willing to bet it's not Rassilon, because why on Earth wouldn't Moffat use Tim Dalton again (and so we would immediately recognize the voice.) Besides the fact that Rassilon just showed up at the end of Ten's life. So not him.
So if it's not Davros, and it's not Rassilon, who is it? I wouldn't put it past Moffat to pull up a character from ages ago (and when I say ages I mean decades and Doctors ago) so Omega and the War Chief are currently sitting at the top of my short list of whose voice that was.
It's got to be someone who knows the Doctor inside and out, who can trick him into a spot where he would be cornered, where his enemies would be fooled into thinking it was a good idea to lock him up in a box. It has to be someone in control of time, who knows everything about it, who could manipulate it and bend it and have it at his will. And so it has to be a Time Lord, someone who slipped through the timelock and is causing problems for the Doctor.
These are important male villain Time Lords from the past who could have built the Pandorica:
* The Meddling Monk (supposedly helped build Stonehenge but totally stupid Time Lord as well...)
* The Master (unlikely because we just saw him last series as villain)
Also has been wiped off my list because John Simm as of this moment is still playing the Master (as he still holds the role according to Steven Moffat,) and that wasn't his voice we heard. Hence, the Master is out of the question.
* Omega (most likely Time Lord on this list)
* Rassilon (unlikely as we saw him last series as villain)
* Morbius (suffered severe brain damage last time he was around and had no real body to speak of)
* The War Chief (hasn't shown up since Two was around and may have turned into the Master)
* The Valeyard (Future incarnation of the Doctor himself causing problems?)
Annnnnnd: The Doctor himself in a different incarnation, not the Valeyard but knowing that at this point he needs to lock himself in a box and cause changes in the Universe. Unlikely, but hey-this is the Happy Theory Land, where all theories are allowed to frolic.
The voice is either Omega (maybe), the War Chief (kinda unlikely) or Davros (probably not, but I had to put what a lot of people are thinking.) I don't think Davros is that smart, honestly, and I don't think he knows THAT much about time and space (he's a geneticist, remember) to be able to set up a scenario/trap/prison for his greatest enemy and all that. Even with the Daleks' (no idea how to punctuate that at ALL) help (and since they hated him last time around they're not on his side or willing to work with him, even if they are reborn I would assume they remember what happened before) he probably wouldn't be able to set up the intricate series of events that have led us to this point.
I still say we're dealing with someone majorly in control of Time and Space and who knows the Doctor inside out and backwards. Someone who can make a box completely inescapable for the universe's brainiest and sneakiest and slipperiest being. He's the Doctor, for heaven's sake. He's escaped every single situation they've ever stuck him in-locks usually can't stop him or slow him down for more than a couple of minutes. He needed Rory to get him out and put Amy in, meaning if Rory had refused the Doctor couldn't have managed to get out by himself.
When River examined the Pandorica, she saw a whole HEAP of locks and blocks and timeholds...everything whoever made it could throw at him to stop him getting out anytime soon. He couldn't get out on his own on this one-who do you think could make a box like this?
I think we're soon to find out who built the Pandorica to house the Doctor...and they might not be very nice creatures.
A theory is like a good salad. There are a lot of bits, I like them tossed with a nice tasty dressing, and it should be shared with others.
Feel free to toss me a comment and mention your own theories.
Ta,
Bec
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