Theory:Doctor Who television discontinuity and plot holes/The Pandorica Opens


 * Why are the Slitheen mentioned as enemies? River lists them as one of the groups coming to witness the opening of the Pandorica. Technically, the Slitheen are not a race, they are a family (World War Three (TV story)), so it's unlikely that their ships are distinguishable from other Raxicoricofallapatorian ships. So how does River know - since the Tenth Doctor doesn't discuss it with her - that it's the Slitheen, and not just average Raxicoricofallapatorians, who are coming?


 * How is it possible for the Doctor to give Rory the screwdriver to open the Pandorica while he is trapped inside it? The Doctor also cannot travel (supposedly) within his own timeline, which he does to bring Rory the screwdriver (which he couldn't have done since Rory had no screwdriver to open the Pandorica).

The Doctor can travel through his own timeline (otherwise much of history would be locked off to him for having been there already, not to mention the events of couldn't have happened). What he can't do is change his own timeline. If the Doctor's future self doesn't appear in the midst of the crisis then it would be safe to assume that option is probably not available to him, but when the Doctor's future self does turn up he practically has to take that option in order to maintain the. Alternatively, the has already destroyed any sense of history so aside from a sense of past and future, hardly any of the rules apply by this point (note Amy being able to exist after her past self is erased and the lack of Blinovitch Limitation Effect.


 * If in The Time of Angels and Flesh and Stone said that River was imprisoned in the 51st Century, then how was she imprisoned in the 52nd in The Pandorica Opens?


 * So little is known about River Song, it's possible she's still serving the same sentence a century on - or has been imprisoned for a different crime.


 * 5145 is not in the 51st century, it is in the 52nd.
 * River meets Liz 10 in 5145. Liz 10 is clearly older, as Sophie Okonedo's hair was greyed in her appearance, but since The Beast Below was said to take place in the 29th century, the passing of around 2,300 years would make her around 2,600 years old, as she was said to be 300 previously.


 * While scanning Stonehenge, how did River Song miss the Cyberman head?
 * The head was shown to be able to move.
 * There is an image on the BBC website for this episode that shows River holding up the Cyberman head in front of the Doctor and Amy. This suggests she did find the head, but it was cut from the episode.


 * How is the Cyberman able to function without a head inside his "helmet"?
 * The Doctor explained that it was the robotics taking over to find a new head, it is likely that the cybernetic suits are given some form of self-preserving AI when they are created.
 * See for example "The Age of Steel" in which a Cyber-suit can perform basic actions with no organic components.


 * Where had the Auton-Roman Officer been for a whole week?
 * It is implied he was some other place, where he gained the knowledge of Cleopatra's death.
 * Yes, but WHERE had he been and WHY had he been there for a week? Visiting another Roman camp? It would make sense if he had been a real Roman officer, but since they were all Autons it makes no sense.
 * It is possible they have been around for years. Since the Alliance is made up of many alien species which are able to manipulate human events, it seems very likely that they were able to involve the Auton army into Human affairs. His absence however, is not a discontinuity. Also the Nestene were not in control of the Romans until the Pandorica opened, as the Doctor hypothesised earlier; they were the perfect disguise, they believed their own cover story, which meant the leader may have actually gone somewhere with human intentions.
 * Also, the officer might not even have gone anywhere. He may have been programmed to think he had been away for a week; maybe he was lying deactivated behind a tree or something.


 * How is a Roman Gladius able to penetrate a Cyberman's armour when 21st century firearms cannot?
 * It was very rusty and already very damaged.
 * It was not Roman but Auton in nature, so it had had greater strength, just as shown in Rose.


 * If the trap involving Romans, Pandorica and Stonehenge was built from Amy Pond's memories, why are there pieces of Cyberman scattered around?
 * They were guarding the place from the Cybermen's point of view, the trap was organised by the alliance and the Cybermen were acting as sentry.
 * But why was the one, rusty and nearly-destroyed Cyberman needed if the place was already guarded by the Auton-Romans?
 * Trust issues. Cybermen could have been used under Stone Henge because the Romans supposedly wouldn't know about Under Henge and thus would look suspicious to the Doctor if Romans were in the cave on guard duty, also the Romans were not Nestene influence unless 'activated' meaning they wouldn't be reliable and might have ended up fighting the other Romans, again appearing suspicious to the Doctor.
 * That still does not explain why the one Cyberman guarding beneath Stonehenge would be rusty, old and scattered everywhere, including the surface.
 * Perhaps there was a battle many years ago. The Pandorica seems to have been created years earlier given its state, so the Cyberman would probably have been down there just as long. Also, Rory attacked the Cyberman with definate intentions to kill it, implying the Romans were enemies (prior to 'activation') may have attacked it and mutilated it earlier, considering The Doctor noticed scorch marks in Stone Henge presumably from the struggle and its body retreated underground without its head (which followed the Doctor after his group went down there).
 * This may also be part of the trap; the remains may even have been artificially degraded to give the appearance of having been there a long time. It may have all been intentionally contrived to keep the Doctor distracted and help "sell" the illusion that the approaching fleet were all vying for control of the Pandorica.
 * Also, the Doctor says it was "probably beaten up by one of the locals, never underestimate a Celt"
 * The Doctor was expecting interested alien parties - the Cyberman was put there to stop the Doctor suspecting the Romans.


 * How can there be a photo of Rory with Amy in the present if he was erased from time?
 * The Doctor explained that certain things still lived on. He even mentioned a face in a photograph.


 * If the trap is made out of Amys memories, how can the Auton-Rory remember his death? If the memories were taken before he was sucked into the Crack, he would not have been dead in her memories. If the memories were taken after Rory had been sucked into the Crack then Amy would not have remembered him at all.


 * Psychic residue was mentioned. Perhaps it has a psychic link to Amy, no matter where and when she was.
 * There's also the possibility that Rory's consciousness somehow survived the Crack and is floating about the the multiverse, coming to the Auton Romans on its own -- drawn by the presence of Amy. In other words, he's not a planned part of the trap, but a flaw in it to be exploited in the next episode.
 * It is possible that Rory was put there by the alliance as part of the trap. Trying to squeeze Rory into the explaination of the site could potentially throw the Doctor off course. All this gives them more time to spring the trap.
 * It appears from what happens in the following episode that it is not exactly the case that all the attributes of Auton-Rory were drawn from Amy's memory (His physical form was, surely, just like the physical forms of the other Autons). Rather, it is the simple fact of Amy's memory that causes him to exist, and also which causes him to be different from the other Autons.


 * Why were the Judoon among the Doctor's enemies?
 * They all teamed up because they believed that the Doctor was going to destroy the universe, so it doesn't matter if they like him or not, they all want him gone so that they can and everyone else can survive.
 * But surely not all these species are needed to form an alliance? Some might not even have time travel technology. In fact, why don't the Daleks disintegrate the Doctor instead of imprisoning him. They do not even need such an elaborate trap.
 * If you watch every Doctor Who story that has ever featured the Daleks, they never just shoot him, and reason is that by this point they must have cottoned on to the fact, if the enemy tries to kill the Doctor, he always wins, it might be from a plan, from a trick or its just luck, but he always wins. The only times that the bad guy gets close to winning is when they don't try and kill, but instead trap him somewhere, of course always gets out, but they get close to winning, and presumably they have realised this, so that's why lock him in an inescapable box.
 * The Judoon are space-police, they would be interested in preventing the destruction of the universe. They are not always on the Doctor's side - as with the stolen planets - because they have different methods.


 * Can't the species make their own trap instead of using Amy's memories? They have conquered galaxies, they can make their own trap.
 * Yes, but if you watch previous storys the Doctor always breaks out of their traps, so probably they didn't want to risk it
 * Either that or perhaps they couldn't decide on one.
 * Also they said that it was "A trap the Doctor couldn't resist". They proberly thought the Doctor would be more convinced and more curious that it was something to do with Amy that he would quite easily fall for it and not think it would be a trap for himself.


 * Whose love is it "that lasts a thousand years"? If it's talking about Amy and Rory, they're two thousand years away from Rory's "death", and in the wrong direction.
 * It's Rory's, he guards Amy for two thousand years in the second part.


 * Despite what she said in DW: The Time of Angels, when River pilots the TARDIS here it does make the dematerialization sound.
 * River says, "Doctor, there's something wrong with the TARDIS, like something else is controlling it." So she may not have caused it to make the dematerialization sound. But in this episode, she also says the Doctor taught her how to fly the TARDIS which directly contradicts her statement in DW: The Time of Angels. So it's also possible she learned the incorrect way from the Doctor and sometime later, she "had lessons from the very best."
 * In The Time of Angels, it was pretty clear to me that River was just teasing the Doctor, and had in fact learned from him.
 * The River Song you see in The Pandorica Opens has not yet been to the Byzantium, meaning she has not yet learned to properly pilot the TARDIS.
 * There was no indication that she has not learned yet, but there is substantial evidence that she has.
 * River Song clearly mentioned that she had learned how to fly the TARDIS in the episode. In DW: The Time of Angels , nowhere in the episode does she say that she didn't learn from the Doctor. Plus, the Doctor is the only one capable of flying the TARDIS presently so by elimination she must have been taught by the Doctor.
 * River Song did mention that she learnt from someone else, the line, "I was taught by the best, shame you (The Doctor) were busy then" seems to clearly show that she learnt from someone other than the doctor. Also the elimination theory is flawed, as she says she remembers the opening of the pandorica at the Byzantium this happens before the Byzantium incident, therefore somebody else may have come along who could fly the TARDIS in the interim, therefore elimination does not work in this case.
 * She states directly here that the Doctor taught her how to pilot the TARDIS. She either got additional lessons from someone later on, or she was simply teasing the Doctor in The Time of Angels (as she often is seen to do). The facts have not been shown as of this point. As for the dematerialisation sound, the Doctor has landed the TARDIS without making the sound on multiple occaisions, so her "parking break" comment in Angels was presumably only a cheeky quip.
 * It is found out in the next series that River learns to fly from the TARDIS itself, being conceived in flight. The fact that the TARDIS was being hijacked at that point gives the reason for extra sounds...


 * Why are the Weevils, Uvodni and Blowfish against the Doctor, they have never met him so why do they have anything against him?
 * He probably encountered them in off-screen adventures. Also they may not nescessarily be his enemies, they like the Judoon may merely want to stop him destroying the Universe.


 * The Doctor says the cliff-face with Hello Sweetie written on it was made of diamond, however the cliff-face was brown and mud-like.
 * If you look closely, the part River Song wrote on was rock, but diamond seemed to be crystallising on the rock's surface above and below the graffiti.


 * River Song was imprisoned in Stormcage before the crash of the Byzantium (from her point of view), so if she had killed the Doctor this would of had to occurred before the Pandorica Opens from her point of view, meaning she can't of killed him, because she was already in.
 * It was never stated that river killed the doctor but even if she did the Pandorica incident is not the first time river has met the doctor, infact she seems very familiar with him, so she could have killed an older doctor (later in the doctors timeline, but earlier in hers).


 * At the very end of the episode, everything in space fades away quickly followed slowly by the Earth. How is the Earth visible if the stars have all gone? There should be no light, so we would not see anything at all.
 * Artistic/dramatic license?
 * There is energy stored on Earth, as the stars Supernova-ed on the 26/6/2010, so we will have still had electric lights. When faced with darkness, solar-activated street lanps will have illuminated across the globe, creating a dim light pollutionny haze around our atmosphere. The question you should be asking is why was the Earth not destroyed when every star in the universe (inc. our sun) supernava-ed.
 * Is it clearly shown that our sun is destroyed? The way the Earth is lit suggests that the sun is behind the camera, and may not have supernova-ed yet. Also, the light from the sun takes about 8 minutes to reach the Earth, so it's correct that it is still visible even if the sun has just been destroyed.
 * Best not to expect realism. Realistically, none of the supernovas would have been visible from Earth for several years, and even if every star blew up at the same time, from Earth it would appear that they went out one-at-a-time, over a course of several thousands of years. That's lightspeed, for you!
 * The Doctor cautions that when the TARDIS explodes, "Every sun will supernova at every moment in history." We might understand that to suggest that from any point in space and time, it would appear as if every star exploded simultaneously, entirely in spite of the fact that it oughtn't to be possible (For every star to explode at every moment would require each star to explode an infinite number of times). As time itself is being destroyed, the normal rules are pretty much right out.
 * Additionally, as is shown in the next episode, the TARDIS explosion provides a sort of "artificial sun" to light and heat the Earth.


 * If a Cyberman can walk, talk and fight without the need of a human head, why do any of them need human heads?
 * The Cybus Cybermen seem to have a back-up system designed for self-preservation in the event that their organic components become compromised (such as the head being severed completely). They don't NEED a head - they want one in order to reach perfection. It has already been established that the Cybermen desire to be the ultimate species, combining the organic with the artificial and "upgrading" until they reach (in their mind) that point. They can function without a head/brain in a limited capacity, a sort of "back-up" system until they can find a new one.


 * Julius Caesar was murdered in 44 BC, Cleopatra died in 30 BC, and the story takes place in 102 AD. It is absurd that the Roman soldiers believed they were being visited by Cleopatra and Julius Caesar.


 * This is more of a character error than anything - we don't know how long the Auton Romans have been in Scotland for and whether or not they have any contact with the rest of the Empire. Add to that the fact that their very existence was due to the Nestene Consciousness interpreting a children's book from Amy's memories, which they were constructed from. They may have very limited knowledge of the events around them at the time, and although they are "genuine" in the sense that they believe they are the Roman army it's impossible to determine how detailed their perception of their "lives" were. Also, at least one of the soldiers were subjected to River's hallucinogenic lipstick; who knows how many more she "convinced"?
 * Maybe the programming used specifically looked for potential Doctor behaviours. When found they would them subtly work towards getting him to the trap. Bad name dropping like this is within the character of the doctor. The Autons would then overlook the absurdity of the claims, and instead help the Doctor and his companions get to the Pandorica.
 * The Doctor is called "Caesar", not "Julius Caesar"; Caesar was the title given to the Emperor, or Dictator for Life. When the Auton-Roman General arrived, he makes a point of pointing out that Cleopatra has been dead for a long time.


 * When the Doctor and crew were galloping towards Stonehenge, they passed camera view with jingling metal stirrups. Metal stirrups are at least six hundred years in Britain's future from this time, and I don't even think they even had old-style rope ones either. Given the fake nature of the Romans in the episode, I suppose we could consider that a clue that the Alliance didn't have all the details right, though I would presume the meta-reason is so the actors could ride the horses properly (or the Doctor Who production team just forgot!)
 * The Doctor probably grabbed some stuff out of the TARDIS.


 * In order for an Auton duplicate of a real human being to continue to function, that person must be kept alive. It may be easily understandable that the rest of the Autons are generic Romans and their officers pulled from a children's book; but we have a problem when it comes to Rory. If indeed this is an Auton Rory, how is it functioning? Duplicates of real people use the telepathic link to have access to all of their memories and such, and Rory no longer "exists", or, as I believe the Doctor's words were, he's "outside the universe". I know this is stretching to be more than a simple plot hole (leading into a better description of the cracks, perhaps), but it's a glaring one from what I can tell.
 * How is the Romans being pulled out out of a kids book is any more understandable than Rory-Auton being made from Amy's memories of him they got from her house. Which in itself sounds crazy to me but this is Doctor Who and these are supposedly beings who's abilities and technology are far beyond what we know of.
 * Rory is not an Auton Duplicate in the usual sense; he was "programmed" with a complete set of fictitious "Roman" memories in addition to his own human ones, up to the moment of his death. Further, he was not created with the intention of being a duplicate. That he has Rory's memories at all is currently inexplicable.
 * It's pretty clearly implied in previous stories that the Nestenes don't need to keep a human alive to have a convincing Auton duplicate, it just helps. In this case, they have the psychic residue from Amy's house, plus potential assistance from whatever extra-advanced technology may have been provided by their Alliance partners (such as the Daleks).
 * The Doctor says in the next episode the time field was pouring the time vortex into Amy's head. This could include Rory's memories.


 * Is the unmaking of the universe the normal result of a TARDIS exploding? It seems like this would have made the Time War rather short.
 * It is never stated that any TARDISes explode during the Time War. Plus, the creepy voice that said "Silence Will Fall" before the TARDIS explodes could cause a larger explosion than usual - destroying the heart of the TARDIS and "unmaking" the universe. Also its possible that the TARDIS exploding on 26/06/2010 in Leadworth creates a bigger explosion than a Tardis would normally make due to whatever weird stuff has happened/is happening at that date and time.
 * Also, remember that the Doctor explained that before the LGTW all TARDISes were powered by a connection to the Eye of Harmony, while since then his TARDIS is self-powered, which probably makes a big difference.


 * River said that there were Cyber ships, but Cybus Cybermen appeared in the episode. The Cybus Cybermen aren't a space travelling race, so where were the Mondasian Cybermen?


 * They may have upgraded their technology to include space (and possibly time) travel, and/or the other Cybermen may have simply not teleported down to the surface.
 * Though we are inclined not to think of the CyberKing in those terms, the Doctor describes it as a kind of spacecraft, suggesting that the Cybermen have indeed developed at least some early form of the technology for space travel.
 * Also there is no reason to assume that only the Cybus cybermen were present. Both spieces could be present (though if this is true then it would seem both have cyber ships).
 * Moffat has said that these were supposed to be Mondasian Cybermen, not Cybus Cyberman. So it is not clear whether that is the case - and if so why they seen=med to have Cybus logos - or what.


 * Why were the Autons in this episode not noticeably plastic as the plastic Mickey was in Rose? As such, why did the Doctor not even recognize that they were not human in the first place?
 * As the Doctor said they are the perfect disguise, even enough to fool the Doctor, they would be more convincing than the plastic Mickey.
 * Also, the plastic Mickey was created in a short amount of time. The Romans could have been created over a course of years, getting their looks correct and human-like.
 * Also these autons are alied with greater and smarter races like the daleks, who would/could have given them more advanced technolagy to make more advanced autons.


 * Why did the Daleks refer to the TARDIS as the TARDIS, when that's just what Susan named it, instead of being the standard name for Gallifreyan time machines?
 * The Daleks have encountered the Doctor enough times to know what his ship is called plus the name TARDIS has been used to describe other Timelords ships too. If Susan did come up with the name like she says then it must have become widely used by timelords at some point.
 * The Daleks have used the term TARDIS in many episodes.
 * In "The Chase" they even sang a Tardis song, which consisted of them repeating "Tardis, Tardis, Tardis."


 * River seems to need no introduction to Amy when she meets her as Cleopatra, though in her timeline River has never met Amy before.
 * We do not know that the Doctor and Amy will not meet River in their future and her past. This is perfectly plausible.
 * "Impossible Astronaut" and "Day of the Moon" take place before "The Pandorica Opens" for River Song.


 * Would nobody in the art world notice that Van Gogh had apparently painted a police box around 50 years before they existed in that form?
 * It was hidden in an attic, as is stated.


 * Bracewell is wearing his black leather glove on one hand, which suggests that this is after he has been exposed as an android. However, wasn't he supposed to have fled following the events of Victory of the Daleks to find his long lost love?
 * Maybe he hasn't "fled " yet


 * He kept in contact with Winston in case he met the Doctor or something. When he discovered the painting, he probably went to the Cabinet war rooms to show him. After delivering it to the Royal Collection, Bracewell left again.


 * He's a genius, there's a war on, and Winston Churchill knows where he lives. He may simply not have been allowed to follow the Doctor's advice in a timely manner.


 * How come Amy cannot remember the Cybermen, despite meeting them in Blood of the Cybermen? Any theories? I think it could be something to do with a Time Crack.
 * Just as a side note: Chelonians only appeared in non-TV stories and are mentioned as one of the species part of the Alliance. Thoughts? Opinions?
 * Blood of the Cybermen occurs after The Big Bang. Although Rory is not with them, they may have dropped him off somewhere.
 * Amy is slightly preoccupied with being converted into a Cybermen, so its unlikely she'll say "Oh, just before you convert me, I've seen you before."
 * The Cybermen in Blood of the Cybermen are different to the ones in this episode.
 * The writers of the TV series don't accept everything from non-TV stories as canon. They pick and choose which adventures/stories/races to refer to, and which to ignore
 * I'm pretty sure Steven Moffat himself claimed that it was canon, or at least someone in production. At any rate, a metallic dismembered arm firing lasers from a distance didn't necessarily scream 'Cyberman', it's not like they ever exhibited such behaviour in 'Blood' and I think it would have been reasonable to say 'what was that?' Even if one did have an encounter. Also, didn't Amy more directly ask what Cybermen were in 'blood?' I think that would rule it out being set after...
 * I'm pretty sure Steven Moffat himself claimed that it was canon, or at least someone in production. At any rate, a metallic dismembered arm firing lasers from a distance didn't necessarily scream 'Cyberman', it's not like they ever exhibited such behaviour in 'Blood' and I think it would have been reasonable to say 'what was that?' Even if one did have an encounter. Also, didn't Amy more directly ask what Cybermen were in 'blood?' I think that would rule it out being set after...


 * When Edwin Bracewell shows Winston the painting he moves his hand with the black glove on - thats the hand that got blasted off by the Dalek.
 * The glove could have been a replacement hand which looks like a glove


 * The Doctor says the TARDIS can translate anything. Thats not true it couldn't translate the words of the Beast (DW: The Impossible Planet) because it was not known by the TARDIS. The writing on the cliff face on Planet One couldn't be translated by anyone not even the Time Lords so the TARDIS therefore shouldn't be able to translate it.
 * The reason the Beast's language wasn't translated was because it pre-dated the known universe. Anything from this universe can be translated by it.
 * But the Doctor said that no one ever could translate the writing on the cliff face, that includes the Timelords. And don't say that the Doctor was wrong. Because if the Timelords knew then the Doctor would know.
 * Keep in mind that the idea to translate the cliff using the TARDIS only recently occured to the Doctor, regardless of him been travelling for what is presumably centuries. Granted, someone with a far less busy lifestyle could have thought of it earlier, but the number of Time Lords who had left Gallifrey were always implied to be pretty low (and often called 'renegades' for a very good reason, meaning that it probably wouldn't come up in conversation). While Time Lords are known to observe the rest of the universe from Gallifrey, the Doctor's visits there usually encourage him to have other things on his mind... Not to mention the visits themselves are usually reluctant and brief. And yes, its very probable that some Time Lords knew while the Doctor was living there in his first incarnation, but that didn't necessarily mean the Doctor personally even knew about the cliff, there are humans who don't know every last location on earth, and considering how large and complex the universe is... Well, it could have easily just been a piece of random trivia that he hadn't picked up... One that was lost upon the extinction of his people.
 * Keep in mind that the idea to translate the cliff using the TARDIS only recently occured to the Doctor, regardless of him been travelling for what is presumably centuries. Granted, someone with a far less busy lifestyle could have thought of it earlier, but the number of Time Lords who had left Gallifrey were always implied to be pretty low (and often called 'renegades' for a very good reason, meaning that it probably wouldn't come up in conversation). While Time Lords are known to observe the rest of the universe from Gallifrey, the Doctor's visits there usually encourage him to have other things on his mind... Not to mention the visits themselves are usually reluctant and brief. And yes, its very probable that some Time Lords knew while the Doctor was living there in his first incarnation, but that didn't necessarily mean the Doctor personally even knew about the cliff, there are humans who don't know every last location on earth, and considering how large and complex the universe is... Well, it could have easily just been a piece of random trivia that he hadn't picked up... One that was lost upon the extinction of his people.


 * If the crack has already expoded at every piont in space and time, then a) why has the entire series happened? and b) why does total event collapse happen in the time of the episode? It should have already happened.
 * Wibbly-Wobbly Timey-Wimey. Time is relative.
 * The cracks are paradoxical in nature, in that they can remove the cause of an event and leave the effect. Amy existed when her parents were retroactively removed from time, Rory continued to be seen in a photograph after he was removed from time, even Amy's childhood self being erased didn't stop her present self from being maintained. Still, after the cause was erased, the effects would have gone too eventually, considering the effect was gradually spreading... Earth was just the last planet to go.
 * From the reference point of most of the universe at that time, the entire series no longer has happened. (Actually, there no longer _is_ a "most of the universe", but you know what I mean.) But from the point of view of the omniscient 3rd-person observer following the Doctor around (that is, you), it still has.
 * From the reference point of most of the universe at that time, the entire series no longer has happened. (Actually, there no longer _is_ a "most of the universe", but you know what I mean.) But from the point of view of the omniscient 3rd-person observer following the Doctor around (that is, you), it still has.


 * Why would time running out cause the Doctor's enemies to physically change matter into stone? It makes no sense.
 * This is only a theory, but perhaps it was more like dust, as some of the figures were falling into piles of dust. Even though it was called a Stone Dalek, it's probably more a welded mesh of dust remnants.


 * Why did the universe only start to run out after the TARDIS exploded, if the cracks were all throughout time?
 * You're thinking of linear time again. Remember, wibbly-wobbly timey-wimey. The cracks hadn't always been all throughout time, they only recently started appearing all throughout time after the TARDIS exploded. It's just like any other episode--in Victory of the Daleks, the Daleks hadn't been in 1941 the last time the Doctor visited, but now they have been.


 * How come the Doctor's enemies all turned to stone, but nothing else did, not the Doctor himself or his companions?
 * Things that were closer to "the eye of the storm" lasted longer. The Doctor, Amy, etc. were all much more intimately connected than, say, a random Dalek. Eventually (and the Doctor implied it wasn't far away), they too would have been affected.


 * If the inside of the TARDIS is another dimension, how did a crack appear in the screen?
 * It was implied that the cracks were affecting all universes - therefore other dimensions.


 * The Silurians live underground, so how can they be in space, and why would they have spaceships?
 * Other species without spaceships (Weevils and Blowfish among them) are seen, so it's likely that they just hitched a ride with one of the more major species involved in the Alliance.
 * Also, these could be Silurians from the future, after they've returned to the surface and gone out into space.


 * How are all the Doctor's enemies in 102AD? I don't think they all have time travel, if it was that common there would be a lot more problems.
 * They hitched a ride with someone who _does_ have time travel. Once, say, the Daleks agreed to join the alliance, why wouldn't they agree to give their allies a lift?
 * The cracks in time linked certain parts of space, maybe they also linked certain times together. If all the cracks radiated out from the explosion, maybe they could be followed back to 102 AD.


 * Why did River Song go in the tardis in the first place?
 * To get the TARDIS to the Pandorica and the Doctor (he needed the resources).
 * I can't remember that being mentioned by the doctor
 * Then you need to pay closer attention.
 * "Now hurry up and get the TARDIS here, I need equipment!"
 * "Now hurry up and get the TARDIS here, I need equipment!"


 * This episode confirms (as if there was any doubt) that the Eleventh Doctor was present when the Pandorica opened, an event which is referred to by River in Flesh and Stone, in which she has already experience these events. However, if she has already met the Eleventh Doctor in The Pandorica Opens (and later/earlier stories), then why does she say in The Time of Angels that the Doctor has "gone all baby-face"? The Doctor does look slightly younger in The Time of Angels than in The Pandorica Opens (since the former episode was filmed earlier), but surely not enough to prompt such a comment.
 * River may be pretending to have never met the Eleventh Doctor, for whatever reason.


 * When River arrive to Amy's room and find all the items that used to create the trap for the doctor, among them there is also a photo of Amy in a police uniform and Rory as the Centurion and it's how they were dressed in there honeymoon at A Christmas Carol. How can there be a photo of them there from something that happened only later after the Doctor reboot the universe and toke them with him on the TARDIS again?
 * It's not a picture of their honeymoon, they had probably dressed like that before for a party or something.


 * When River opens the TARDIS doors before the TARDIS explodes what is the thing blocking the doorway?
 * Probably the TARDIS's organic "skin". Perhaps the TARDIS has "closed over" the doorway, like a wound.


 * The Pandorica is supposed to be an ultimate prison with loads of security to prevent its prisoner from ever being released. The sonic screwdriver opens it without a problem. Why can't an alliance of countless extremely advanced species come up with a prison that can't be opened with a device they all know the Doctor has?
 * Because a prison is not meant to keep people out, but people in.
 * Preventing people on the outside from opening the prison to let the person on the inside escape seems like it's been a standard of prisons since their inception, at least on earth. I'm sure a coalition of so many advanced species should be able to imagine a scenario where someone tries to break the Doctor out.