This post contains spoilers for everything up to and including the latest episode, The God Complex (which I thought was fairly decent). It's also frigging long, but I hope you find it interesting.

(EDIT - on top of this, Camilla has contributed something that has lead to what might be our best theory yet. Check the replies to read about it. It's still based on some of the stuff in this main post, so read that too.)

My friend and I noticed something while watching the episode, something that made us open our eyes wide and threw into question a lot of what we've been seeing this season. This has prompted me to go back and look through things again, and with the help of a few observations from fan sites, I can theorize that there might be a lot more going on that we've understood yet. Or I might just be overanalyzing. You can decide!

The thing that sparked this was a scene right near the beginning of The God Complex. The Doctor is astounded by the level of realism in the fake hotel and he grabs an apple, picks it up, takes a big bite, then chews it happily and moves on.

But do you remember the start of Moffat's run? The Doctor crashes into Amy's yard and asks for an apple. When he takes a bite, he spits it out because he apparently hates the taste of apples in this new body. "New body, new rules," he tells Amy.

So unless this was just a mistake on the show's part (and Moffat seems to be very good at throwing in little things that you might want to call a mistake because they're in the background and no attention is called to them), it seems that something is up. Why did the Doctor's tastes change?

If you go back further, this isn't the first time there's been something weird going on with food. At the beginning of this season, the Doctor who is (apparently) 1103 years old tries a sip of wine at the lakeshore. "I'm 1103," he says, "I must have tried it sometime." After finding it not to his liking, he says that he thought it would taste like the gums.

But ... in The Lodger, the Doctor tried wine, and didn't like it. Does he just not remember? Or is there something else going on here?

In the episode Night Terrors, the Doctor picks up a Rubik's Cube while talking to the boy, and attempts to solve it. After a moment of fiddling he is unable to solve it and tosses it away, declaring that he hates those things.

In The God COmplex, the Doctor finds a Rubik's Cube in the hotel. We see it only very briefly. Near the beginning he picks it up off a counter and it is clearly unsolved. Later in the episode we see a brief flash of it again. It is now solved. Was he simply determined to solve one to prove he can? Did he somehow gain the ability to quickly solve it while distracted by other things? Or again, is there something else going on here?

"Silence will fall."

The last two seasons of Doctor Who have had different main plots arcs, but have been connected by overall mysteries that have yet to be resolved. If the mysteries are all connected in some way, or at least if their resolutions are connected and will still be shown, then it may be worth recounting them. Let me know if I missed any.

1. Something has the ability to hijack the TARDIS and make it explode. It did so at the end of The Pandorica Opens, and it did not seem to mind that this caused the universe to end. Whether this entity or person also played a role in convincing the Doctor's enemies to band against him and lock him in the Pandorica remains to be seen.

2. "Only the Doctor can fly the TARDIS." This is why the Doctor's enemies locked him away. They said that they had determined that a TARDIS explosion would destroy the universe, and they believed that only the Doctor could fly it. We've seen this to not be quite true. River can fly it because she was born on it and it showed her how. But it begs the question of why his enemies were so certain only he could fly it, and that he would be to blame for its explosion.

3. "A good man. The best I've ever known." This is River's description of the man she killed (is going to kill). The Tesselecta had information from the future that she is the one who kills the Doctor at Lake Silencio, and thus the one in the astronaut suit. That doesn't mean that information is correct, though, and when Moffat gives us an answer we are often wise to look elsewhere for the truth.

4. The Headless Monks were in the museum at the end of season five. When adult Amy emerges from the Pandorica to find child Amy there, you can clearly see dark, robed figures hiding behind the sarcophogi along the wall. They make no attempt to interfere, but they clearly move. They are not shadows cast by the sarcophogi. As the camera pulls back away from the Amys, a bit of dark robe enters the screen on the right side, in front of the camera, and then pulls away. It was them. What were they doing there? This was taking place in a pocket universe Earth where everything else had ended and people were vanishing all the time.

5. A mysterious glimpse of the Doctor. This one is very hard to catch, and I don't take credit for it. I read about it elsewhere. In The Big Bang, the Doctor from briefly in the future uses his time travel device to quickly hop into the past to leave messages for Amy, to talk to Rory, and to grab Amy a drink. Throughout this sequence, the Doctor is wearing the fez that he picks up from the museum (fezzes are cool). He wears it in every single time jump, because he's wearing it when Rory first tells him about the fact that he jumps back in time looking like that.

But if you look very closely, when child Amy enters the museum and goes into the Pandorica room, the camera shifts to a view in front of her as she pushes into the crowd, a smile on her face as she finds the Pandorica, and as the crowd opens behind her we see, just for the briefest of moments, the Doctor. Standing behind her, glancing at her, and adjusting his tie as he quickly vanishes off-screen. He is not wearing a fez. It's possible that this one really is a mistake, but Moffat has pulled sly, quick wardrobe clues in the past with the Jacket Doctor. If it's not a mistake, what the hell is a non-fez Doctor doing there?

6. "I'm sorry." The Doctor's last words as an impossible astronaut rises from the water and strikes him dead. Moffat says that it really is him and he really is dead. We don't yet know how he's going to get out of that one. The Tesselecta says that this death is a fixed moment in time that cannot be changed. Who was in the astronaut suit? River is the obvious suspect, and the one fingered by the Tesselecta, but that doesn't mean it's actually her.

7. There is a mysterious figure standing behind a shed at Lake Silencio, watching the Doctor's death. We have no indication who it was.

And now we have this whole food thing as a new mystery. What does it all add up to?

[Doctor]: Nothing can get into this box.

[Rory]: You got in there.

[Doctor]: Well, there's only one of me. I counted.

But what if there isn't? What if there's a second Doctor?

"Hang on, kid. This is where it gets complicated."

I'm a foolish theorizer, because I already once predicted the existence of a second Doctor. I made this prediction here before the end of season five, to explain the Jacket Doctor. I was right in a way, but oh so wrong about the execution and the explanation. But here I go again. Back to the old two Doctors well.

We've been given two potential explanations for how the Doctor who dies in The Impossible Astronaut might not be the real one. We've seen a ganger Doctor and we've seen that the Tesselecta can replicate a person. Since we've been given more than one possible answer, the real answer must be something different. And as noted earlier, Moffat says this is the real Doctor. It's possible that Moffat is a liar, but hey.

At the end of The Big Bang, the Doctor reboots the entire universe, causing himself to be erased in the process. Amy and Rory forget about him, though River appears to remember, because she shows up at their wedding and leaves the blank journal for her. This is probably because she's a heavy duty time traveller. The Doctor remembered Rory when the cracks swallowed him, after all.

Amy then remembers the Doctor, and pulls him back into existence in the brand new universe. How did this new universe work without a Doctor, though? If the whole universe started from scratch and there was never a Doctor, would the Earth even still be alive? There have been so many threats that he stopped. Was there never ever a Doctor there until Amy restored him?

Or perhaps was there a different Doctor in that new universe, one who did slightly different things, one who didn't meet Amy and Rory, one who took a different path and became a slightly different person? And then Amy remembers the old Doctor from the old universe and pulls him into existence in the new universe?

Obviously there are a lot of problems with this idea, and I'll go into some of them, but let's play with it for a moment. If there was a different Doctor, he might be a slightly different person. He might enjoy Rubik's Cube puzzles. He might like apples. He might wear a different coat. At the beginning of Let's Kill Hitler, the Doctor shows up wearing a longer coat than usual. Maybe he just changes coats sometimes. By the next episode he's back in his old tweed jacket.

The Silence, a group of people who believe silence will fall when the first question is asked, hate the Doctor. They call their fight against him an "endless, bitter war." They train and dedicate themselves to beating him. They kidnapped Amy and raised River with brainwashing to kill him. But who are they? Where did they come from? Why do they hate him? Why do they think he's a mighty warrior?

What if the new Doctor from the new universe is indeed a mighty warrior? Someone who has made slightly different choices and became a slightly different person, someone who is hated enough to form something like the Silence. The Doctor is stung by River's accusations that it's all his fault because he makes them so afraid. What if River doesn't know she's talking to a different Doctor? She might not even know there are two of them, even though she interacts with both of them at different times.

But one could ask, wouldn't the two Doctors know about each other? They can sense when there's another Time Lord in the universe. Well, maybe they do. Maybe they sensed each other as soon as the old Doctor was pulled into the new universe by Amy. It's possible they've met and are working together.

"Rule number one. The Doctor lies."

In The Impossible Astronaut, we meet a Doctor who says he's 200 years older than the Doctor we know. But there are indications that this Doctor doesn't know as much as he pretends to. When he and River are synching their journals, River asks if he has Easter Island and he flips through his journal and says that he does. Why does he need to flip through the journal? If he's been to Easter Island with River, why doesn't he just remember that?

It may be telling that it's River who asks about something first, and the Doctor replies passively. He then makes mention of Jim the Fish. River asks what Jim the Fish is up to these days, and the Doctor says something vague (looking almost uncomfortable) about how he's building a dam. River doesn't respond to this. Is it possible the Doctor doesn't know who Jim the Fish is? But how could he know to even mention Jim the Fish in the first place?

Well, later this episode, when the Doctor dies and they return to the cafe to find a younger version of the Doctor, River asks him urgently, "Jim the Fish? Have we done Jim the Fish yet?" To which the Doctor replies, "Who's Jim the Fish?" But he's heard the name now. And he can reasonably suspect that it was used in a recent conversation about things they've done. It is something he might remember for later. The Doctor we see who dies might not be much older at all.

"The Doctor in the TARDIS doesn't know."

This phrase, uttered once by Prisoner Zero and once by Angel Bob, is part of what first made me think there might be two Doctors. It is a curiously specific phrase that seems to suggest that the qualifier "in the TARDIS" is important, as though to differentiate from a different Doctor. The problem with this is that it throws my entire theory about the new and the old universe out the window, because they were saying this phrase before the reboot. The "Silence will fall" phrase predates the reboot as well. This suggests that the reboot and whatever happened in it are not involved in the creation of the Silence, unless they exist in both universes but only hate the Doctor in the new one. And the universe theory does nothing to explain why there might have been a fez-less Doctor in the museum, watching child Amy, nor why the Headless Monks were there.

So where does this leave me? I have no idea. I think it's possible that there is somehow a second Doctor, and that the two of them might be working together for some purpose, and that this could explain how the Doctor could die but still be alive. But I'm still having a hard time explaining how this could be the case, which means I could be out to lunch. I really can't think of anything else to explain the food thing though, and the Rubik's Cube fits in with that as well.

That was a lot of words. Do you have any theories or ramblings of your own? What do you think about the food and the Rubik's Cube? What did you think of The God Complex?

Rory and Amy will probably be back for the season finale. Is the next episode a random episode, or is it the first part of a two-part finale? It seems random, but we must remember that Craig used to live beneath an almost-TARDIS that looked very similar to the one in the past where River and the Doctor killed the Silent Aliens.

(P.S. I also have a theory that there are Silent Aliens on the TARDIS itself, nesting in the rafters as we saw them nesting in the orphanage. Early in The Eleventh Hour, the Doctor looks up and looks very confused for a moment before going on about his business. At the end of the episode Amy is looking up at the ceiling of the TARDIS and starts to panic, until she looks back at the Doctor and everything is fine.)