For European peoples and those in North America like me who acquire the episodes right after they air, the two-part season finale of Doctor Who will begin this weekend. For those of you who aren't caught up, be warned that this post will contain spoilers. Also be warned that this post is ridiculously long. I have provided a tl;dr at the bottom.

It's become something of a tradition in the new series (I can't speak for the old) to seed something sneaky throughout the episodes that comes together in the finale -- Bad Wolf, Saxon, etc. There is a new head writer this year who has written some of the new series' most famously clever episodes, and there are indications that things may be extra sneaky and extra clever this time around.

While it is also entirely possible that we are reading too much into things, the evidence strongly suggests that clues have been seeded throughout the season that will come together in the finale. These don't seem to be the same type of clues as in previous seasons, where simple phrases were strewn about and while the watcher could pick up on them, they had little chance of predicting what they meant. The clues in the current season appear to point toward an actual mystery that we may be able to pick apart before it is revealed.

With this post, I hope to list as many of the clues (or possible clues) as I can, based on my own observations and those of other RAFO viewers, such as ATimp and Brad (farmboy), and also to present my own theory about what it all means and what might happen in the finale. I welcome other theories and other clues if people wish to add them, and I welcome debate or discussion on my own theory.

So. Let's theorize! I'll go through the clues and plot points first. If you just want my theory, skip to the end. Some of this has been talked about before in various episode reaction posts, while other parts are exclusive to this thread based on my latest rewatch.



The Cracks

The cracks have been the major plot device for the season's central arc story. The Doctor has stated that they are cracks in space and time caused by an explosion so powerful that it is tearing the fabric of reality and causing not only the end of the universe, but the end of the entire universe's history. What do we know about the cracks?

Some of the cracks lead to the end of the universe, while others simply provide a gateway between separate points in space and time. The Doctor closed one crack by opening it all the way and letting it snap shut. Another crack was closed when the weeping angels, who are filled with time energy, fell into it. The Doctor stated at the time that he himself would have enough time energy to close a crack, were he to be taken by it.

Sometimes, but not always, a sort of energy seeps through the cracks. Anyone who is touched by this energy is not simply killed, but is, according to the Doctor's theory, erased from time. It is as though they never existed.

It has been stated, in the episode Vampires of Venice, that through some of the cracks there exists only silence. Presumably, this is the silence of non-existence, the silence of a dead universe.

Through one such crack, the Doctor stuck his hand in and pulled out a broken piece of what appears to be the TARDIS.

Rory was taken by one of the cracks, and was presumably erased from time. However, the ring he bought for Amy remained, possibly protected by the TARDIS. When Amy discovered the ring's box and opened it in The Lodger, a crack was shows to open wider as a result. This perhaps indicates that the cracks are related to Amy, her actions, or her emotional/mental state.

This is supported by a scene at the end of Flesh and Stone, where the Doctor exclaimed that everything had to do with Amy. The Doctor has determined that the explosion that caused the cracks took place on Amy's planned wedding day, and stated that the most important thing in the universe was that he get Amy "sorted out."

A crack first appeared, or was first seen, on Amy's bedroom wall when she was seven years old. It was the only thing that frightened her. Cracks have been spotted several times in the same area as Amy; however, the aliens in Vampires of Venice claimed that their world was host to multiple cracks. Unless Amy visited them, it is safe to say that cracks do not exclusively follow her around -- unless, of course, Amy visits their world in the future, opening a crack that allowed them to travel into Earth's past.

Both Prisoner Zero and the weeping angels seemed to know something about the cracks -- either what caused them, or what they are. They each mocked the Doctor for not knowing, using an identical phrase: "The Doctor in the TARDIS doesn't know."



The Jacket Doctor

In Flesh and Stone, there is one scene that forms the basis for all of my speculation, one scene that provides the most compelling evidence that there truly is a mystery to unravel.

In the episode, the Doctor loses his jacket after being attacked by several weeping angels. He runs into the forested section without his jacket, and appears there wearing long sleeves down to his wrists. After saving Amy by having her close her eyes, he rushes off with River and the soldier, leaving her behind, obviously disappointed to be left alone and in the dark, both literally and metaphorically.

Just then, the Doctor's hands reach back into the frame. His sleeves are rolled up, as we can see his forearms. He appears to be wearing a different watch as well (possibly the same watch that appeared on a nighstand in The Lodger, if Brad's catch is correct). In subsequent frames we can clearly see that this Doctor is wearing his jacket.

He tells Amy that she needs to start trusting him, and that it has never been more important. He tells her that he doesn't know what the cracks are but that he is working it out, and he glances in the direction the shirt Doctor left in when he says this. He implores Amy to remember what he told her when she was seven, and says that the point is that she needs to remember. He then kisses her forehead tenderly and leaves.

We then return to the Doctor, without his jacket, shirt sleeves down to his wrists, walking with River.

The conclusion is obvious: there were two versions of the same Doctor in that forested area. One of them is likely from the future. It is known from previous seasons (episodes such as Father's Day), that the Doctor can go back into his own timeline, but that doing so is very risky and can cause grave hazards if anything goes wrong.

This is the only confirmed sighting of what appears to be a second Doctor. A humanoid shape passed in front of the camera near the beginning of the first episode that may have been him -- it was assumed at the time to be Prisoner Zero, but it was later stated that Prisoner Zero needed months to form a psychic bond and take human form. It's possible this was an error in the episode, but it is also possible that this shape was the Jacket Doctor.



The Doctor Unfocused

This may not be a clue, but it's part of my pet theory.

Throughout the season, the Doctor has repeatedly failed to notice things or failed to figure things out that he later seems to think he should have. This could be simple plot convenience -- there is no tension if the Doctor figures something out right off the bat -- but it could be something more.

This has been seen right from the first episode. Here, the Doctor blames his lack of focus on his recent regeneration, a plausible excuse. He fails to notice the perception filter on the extra door in Amy's home, where Prisoner Zero is hiding. He takes great, exclamatory interest in a duck pond later that episode, but can't say why, and is then distracted. He nearly misses Rory's photography.

The Doctor does not realize that the space whale would willingly transport the children, and Amy has to figure it out. The Doctor does not notice that the statues in Time of Angels have only one head, and berates himself for it. In Hungry Earth, he fails to realize that the young boy is going outside by himself. In Vincent and the Doctor, he berates himself for not understanding that the creature is blind. In The Lodger, he has yet another head-smack moment when he figures out what the second floor is.

This could all be nothing. It could also indicate that something is wrong with our Doctor.



River Song

Moffat's own creation, River Song makes her return this year in a much bigger role. We know from the previews that she will take part in the finale.

She is very important to the Doctor, even though he's not sure why yet. They always meet in the wrong order, with River getting younger each time the Doctor finds her from his own perspective, and the Doctor getting younger each time River finds him, from her perspective. She is the only person we know of (or that I know of, discounting the old series) who knows the Doctor's true name. She has been warned by the Doctor not to give his younger self spoilers as she gets older and meets his previous incarnations. She knows how to fly the TARDIS.

We know that she has been imprisoned for the crime of murder. She allegedly killed "a great man, a hero to many." The soldier escorting her seems to think that the Doctor would refuse to help them if he knew the truth.

Given what we have seen this season, this indicates that River "kills" either the Doctor, another version of the Doctor, or a version of Rory that has survived somehow and comes to be known as a hero to many. There are no other recurring male characters this season.

The other possibility is that her crime is a setup for another season, but given that she will appear in the finale, it seems likely that the truth of what she does will play out in the next two episodes.

It has been noted by ATimp that River and Amy have identical watches. Looking at it myself, I can confirm that they seem very similar. Given that they changed the Doctor's watch when he appeared in Jacket Doctor incarnation, this is not likely to be a result of lazy costume designers.

Does this mean that River Song is a grown-up version of Amy Pond? It's possible, but strikes me as an odd solution. They don't look particularly similar, though you could account for the difference with age and hair dye perhaps. River does not have Amy's Scottish accent, which Amy kept through 12 years of living in an English village (the Doctor made note of this in The Eleventh Hour).

It is more likely that Amy, for some reason, gives her watch to River in the finale. This would be a younger River than the one we see in the angel episodes. Whatever that younger River experiences in the finale (and it will be a younger River, because River knew about the Pandorica), she hides most of it from Amy and the Doctor when she meets them later (earlier in the season).

Don't you just love time travel?



The Pandorica

The Pandorica will play a central role in the finale. The Doctor has heard of it before, as he calls it "a fairy tale".

From the season's beginning, we have heard that the Pandorica will open. Prisoner Zero told the Doctor, as did River Song (who had likely already experienced the events of the finale as her younger self).

You all know the myth, I'm sure. In Greek mythology, Pandora was the first woman, and was given a box that she was told not to open. Curiosity got the better of her, but opening the box unleashed all the evils of the world. Only hope remained at the bottom. This myth's parallel can be found in the story of Adam and Eve, where Eve's curiosity in eating the apple caused the fall of mankind.

From what we saw in the preview, we can assume that whatever is held within the Pandorica is so dangerous, or so powerful, that alien races from throughout the universe converge on Earth to either destroy it (if it is dangerous) or claim it (if it is powerful).

What could be so powerful and dangerous? Is it the thing that causes the end of the universe, the cracks, the silence? If so, how is it related to Amy?

We see that even the Daleks appear to fear the contents of the Pandorica. From what little I've seen, we have only known the Daleks to fear one thing -- the Doctor. The Oncoming Storm. However, unless they pull something strange whereby the Pandorica contains (or causes the creation of) the evil Doctor we saw in Amy's Choice, it must be something else. Though the damage an evil Doctor, the last of his race, could cause would certainly strike fear into the species of the universe.

So, what's inside the Pandorica? How does it relate to Amy and the end of the universe?



Themes

Certain themes have crept into the season, seen on multiple occasions. Perhaps some of them cast light on the mystery?

1. Memory

The Jacket Doctor implores Amy to remember what he told her when she was seven. He does not seem concerned with the actual information she needs to remember, but says that she simply needs to remember, as though the act of remembering is what's important.

It has been mentioned more than once that time travelers can remember things that are removed from timelines not their own. The Doctor even says it's possible for Amy to remember Rory if she tries hard enough. She fails, but bits of memory seem to remain lodged in her subconscious.

This could also explain the duck pond from The Eleventh Hour. The Doctor demands to know what it is, and how it can be a duck pond if it hasn't got any ducks in it. He is distracted before he can figure out why that's important. The answer, though, is clear: it's a duck pond because people remember that it once had ducks. Without that memory, it would simply be a pond.

(If there's clever wordplay about duck pond and Amy Pond, I can't unravel it, unless it'll be a simple case of "Duck, Pond!")

This perhaps will play an important role. If someone is eaten by the cracks and erased from time, would they continue to exist somehow if the right person remembers them? Might Rory return if Amy remembers? Might River Song kill the Doctor, and Amy's memory return him to existence?



2. Amelia Pond and the Fairy Tale

"Amelia Pond," says the Doctor. "That's like a name in a fairy tale."

"Amelia's a brilliant name," he says. Amy replies, "A bit too fairy tale."

"The Pandorica is just a fairy tale," says the Doctor. "Aren't we all?" River replies.

In addition, the Doctor has returned to the fact that Amy doesn't go by Amelia any longer more than once. He began muttering about it in Flesh and Stone while trying to save Amy from the angel in her eye, but didn't know what he meant and quickly moved on to new thoughts.



3. Perception Filter

This plot device has been mentioned before in previous seasons, but never has it played such a role as it has in this one. Episode after episode, we see a perception filter used, mentioned, or possibly used. Are the writers setting us up for some sort of major reveal involving a perception filter?

Prisoner Zero used a perception filter to hide its door in Amy's home. The Doctor says that the angels may have been using a perception filter to keep them from noticing they only had one head. The bug aliens in Venice use perception filters. The ship on the second floor in The Lodger is protected by a perception filter.

If this is more than an overused plot device, perhaps something has been hiding behind a perception filter all season long. I don't know what it could be. Unless (and this is a massive stretch) the character of Rory has been the future Doctor hiding behind a perception filter all along. Don't look at me like that, I know it's ridiculous. However, it has been noted (in The Lodger) that a perception filter is more than a disguise; it tricks your memory.



My Theory

My theory is that, once upon a time, Amy Pond destroyed the universe. I'm not entirely sure how; if pressed, I would bet on her blowing up the TARDIS, causing some sort of reaction in the time vortex that leads to the explosion, but it could also be her interacting with whatever is in the Pandorica. Cracks began to spread through time and space. It was the end of the universe.

The Doctor survived. Perhaps he couldn't stop Amy, perhaps he never saw it coming, but he lived. Using the cracks (or the TARDIS if it wasn't destroyed) he travelled back to specific points in his own timeline, places where he knew the cracks existed, and began to manipulate events in the background.

This is where we enter the season. The Doctor we are seeing, the story we are seeing, is the second chance. The future Doctor is operating in the background, careful to avoid direct contact with himself, altering the timeline to give his past self a chance to figure it out in time and stop Amy and/or save the universe.

The future Doctor, the Jacket Doctor, was there from the beginning. He started the TARDIS engines phasing so that the past Doctor had to run out and leave young Amy behind, or he sabotaged the TARDIS so that it wouldn't reappear for 12 years, or he did both. He told young Amelia Pond something that he later, in Flesh and Stone, asks her to remember.

I believe this explains why the Doctor has seemed so unfocused, why he continues to miss things. His own timeline has been altered, causing a skew to his perception that is affecting him.

If this is the second time around, that means that things went differently the first time. What might conceivably have been different? For starters, there would have been no cracks the first time, because the explosion hadn't happened yet.

You could argue that the explosion is a fixed point in time that happened on that date regardless of where anyone else is in their timeline, but that simply can't be true. If it were, the entire universe would already be gone; the cracks would have been appearing all over time already, including in previous Doctor Who stories. The only explanation that works within the logic of the story is that the explosion on Amy's wedding day happened as a result of Amy's interaction with the Doctor.

Put simply, the explosion doesn't happen in the regular timeline of the universe. It happens in the Doctor's timeline, which is an entirely separate thing. It happens because of time travel. So the first time through, there were no cracks.

This means that there was no reason to sort out Amy Pond, which means there was no reason to bring Rory along. Rory may have found his way along anyway, and I believe he did. He was not killed by the Silurians because there was no crack in the wall to distract and delay the Doctor -- they got into the TARDIS and flew away before the lizard lady arrived. Rory lived to be there ten years later, waving at them with Amy from across the valley.

Yet somehow, because of time travel and the Doctor, something ended up happening on their wedding day to blow up the universe.

Things are different this time, both because of the cracks and because of the future Doctor's hand in events. Rory was killed and eaten by the crack (though I believe he will return). The Doctor's relationship with Amy may be different. Everything has gotten very wibbly-wobbly, timey-wimey. But both times it leads to the Pandorica, whatever is within, and Amy's wedding day.

Now I am seriously typed out. I've been writing this thing for most of three hours. Blame that if some of the stuff at the end doesn't make sense. I want to hear your own ideas too! If we end up being right about some things, then we officially win the internet.



Random Miscellaneous End Thought

There are ruby slippers on Amy's dresser. There's no place like home? I also can't shake the suspicion that she was something more than a little girl. The suspicion that there was no aunt, and that Amelia Pond is, perhaps, something from an actual fairy tale. However, this is pure paranoia.



tl;dr - A future version of the Doctor is manipulating events so that his past self can succeed where he failed, and this is the only second chance they get to stop Amy Pond from blowing up the universe and/or TARDIS.