Question: Why does The Master fear The Doctor forgiving him? What's he forgiving The Master for exactly?
Answer: The Master knows that deep down, he deserves death for the crimes that he's committed throughout his life, and since he regards The Doctor as his arch-foe, he expects it to be at his hands. The fact that The Doctor is still willing to forgive him for all of his crimes hurts him more deeply than death would.
Question: This whole finale never made sense to me because of these plot holes. If all the stars were supposed to supernova when the Doctor was locked up, then why was the Earth not destroyed by the sun exploding? He says the world carried on relatively normal due to the TARDIS exploding being a light and heat source to replace the Sun, but the supernova should have decimated the planet regardless, shouldn't it? Also if the TARDIS was exploding at every moment in time and space (as the Doctor states) then shouldn't it also have exploded on earth every time it has been here in the past? Destroying the Earth that should have been destroyed by the supernova?
Answer: The stars didn't supernova, the rest of the universe ceased to exist. Earth still stands because of it's place in the eye of the storm and the TARDIS explosion providing the heat and light that the sun that now never existed would have, but history is still collapsing. Because they are all temporal anomalies, it buys them some time for the Doctor to pilot the Pandorica into the TARDIS explosion, restarting the universe.
Question: In Season 5, the Doctor states his age as nine hundred and six years old. In a voice-over for Season 8, he states that he's lived for over two thousand years. Granted, he's a Time Lord, but how could he make such a grievous error in his own age?
Answer: He has not made an error, he probably is 2000 years old. He may have been 906 in season 5, but remember, at the end of season 6, he is 200 years older, 1107 years old and in season 7 episode 3, the Doctor stated he was 1200 years old. Plus, he also in "The Time of the Doctor", he lived at that village for several hundred years. It may have been only 4 years for the audience, but it has in fact been over a millennia for The Doctor.
Question: 1. Why was Rose not allowed to touch her past self without creating a paradox and causing those creatures to appear and eat everyone, but Amy was allowed to touch her younger self without any repercussions? 2. Why was Rose able to have the time vortex in her head for a few minutes and it only knocked her unconscious whereas the Doctor had it inside him for about 30 seconds and it basically killed him and caused his regeneration?
Answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.
Question: If all the stars have gone out, then how come it is light out when Amelia and her Auntie Sharon are going to the museum? If all the stars had gone out, it would have been dark, since the Sun is a star.
Answer: You are correct, the sun was erased with every other star in the universe.The thing keeping the Earth warm and light is the TARDIS, which exploded and is now exploding at every moment in history.
Question: When The Doctor shows young Kazran his future, older Kazran touches his younger self. He did this without an explosion, however, in 'Doctor Who' it has been said that 'if you touch your younger self, it will create an explosion'. How did the older Kazran, in this episode, touch himself without an explosion?
Answer: It creates a paradox, which isn't always an explosion, but can be. And it doesn't do it in this case for the same reason that the controls no longer operate for Kazran: The Doctor's intervention in his life has caused him to not be the same man he was before.
Question: In this episode the Doctor says 'Metebelis three' different to how Sarah-Jane in 'The wedding of Sarah Jane Smith' (The Sarah Jane Adventures spin-off) says 'Metebelis three'. (she says it like 'Metabeelis'), so which is correct?
Answer: The Matt Smith pronunciation in this episode seems to be the outlier. Metebelis 3 was first mentioned and shown in the Jon Pertwee stories "The Green Death" and "Planet of the Spiders". In those stories, and in Sarah Jane Adventures it was pronounced 'Meh-teh-beel-is'.
Question: How exactly does the 8th Doctor regenerate to the 9th, and how does the Tardis console change?
Answer: The 8th Doctor regenerated into the War Doctor by his ship crash landing on Karn. See "The Night of the Doctor". The people on Karn recognised him and allowed him to have a regeneration because he had helped them before. He got to choose who he regenerated into, and decided on the War Doctor, saying "Doctor no more". The War Doctor regenerated into the 9th Doctor in "The Day of the Doctor" apparently just due to old age, saying "Oh yes, of course. I suppose it makes sense. Wearing a bit thin. I hope the ears are a bit less conspicuous this time."
Question: Is the reason for Amelia's crack due to the fact that in series 7 'Angels take Manhattan' she gets zapped back in time, and the crack is there to put those two parts of her life together?
Answer: No. The cracks in time were caused by the TARDIS exploding on Amy's wedding day. The reason why they were at the locations they were at was because the Doctor was there.
Question: In Season 7 Episode 10 (and others) it's said that the TARDIS has a sort of "universal translator", even after the TARDIS leaves the submarine, they can understand and speak Russian. How come in this episode, they can't understand the aliens, for the most part, as they come out as a bunch of grunts, even though the TARDIS is in the area?
Answer: The only one that grunts is Dor'een, the alien trying to sell the moped. The reason for this could be the same reason why the TARDIS does not translate baby, horse or tree, to the others. A plot device just to show off the Doctor's intelligence.
Question: Between series 5-7, how many times does Rory Williams die?
Answer: In one way or another, eight times. He dies twice in the episode "Amy's Choice", once in each of the two dreams, firstly killed by an Eknodine in the Leadworth version of the dream, then again when the Doctor blew up the TARDIS in the other dream to allow them to escape it. He's then killed by the Silurian Restac in "Cold Blood", shortly before his body is consumed by the cracks in time, erasing him from history completely. He returns as an Auton duplicate, restored from Amy's memory, in "The Pandorica Opens" - this duplicate is destroyed in "The Big Bang" when the universe is reset, although some memories live on in the human Rory recreated in the rebooted universe. He died again in "The Curse of the Black Spot", but was successfully resuscitated by Amy. He's seen to die of old age in "The Angels Take Manhattan", then kills himself in the same episode by jumping from a high roof (as does Amy) to set up a paradox to eliminate the Angel threat. He then finally dies off-camera at the age of 82 after having been sent back in time by a surviving Angel, having lived out a long and happy life with Amy.
Question: If Amelia can remember the people in 'flesh and stone' when they stepped into the 'W' crack, how come she can't remember Rory after he is taken at the end of this episode?
Answer: The Doctor said Amy remembered the clerics because they weren't part of her life, but Rory was. That's why the clerics forgot about the other clerics, because they are part of each other's lives. So you can still remember people being erased from time if they are not part of your life.
Question: When they are talking about the Daleks at the end of this episode, this is what they are saying: DOCTOR: It's not that. There's something else. Something we've forgotten. Or rather you have. AMY: Me? DOCTOR: You didn't know them, Amy. You'd never seen them before. And you should have done. You should. (They go inside the Tardis and it dematerialises, revealing a glowing w shaped crack in the wall.) My question is: What is the Doctor meaning by what he is saying to Amy?
Answer: The Doctor is referring to the events of the two-part finale of the fourth series of the relaunched show, "The Stolen Earth" and "Journey's End". These episodes featured a major Dalek invasion of Earth, something that Amy should remember. What concerns the Doctor, leading to the conversation you refer to, is that she apparently doesn't, because if she did, she'd have recognised the Daleks the moment she saw them.