I've heard this theory before and I really like it. Maybe it's because of my undying love for characters to secretly be evil(my inner psychopath is enjoying herself a lot). Until the day Moffat proves me wrong, I believe that everything that happened in the last two series(TARDIS exploding, Melody and Amy being kidnapped, Doctor "dying") was the work of, either Master, or Time Lords. They would be the only ones who are capable of something like that. They know Doctor, his darkest secrets and worst fears and they are pissed off.
On the other hand, as much as I love good old Moffat, I don't think he has the balls(pardon my language) to make Rory into Master. That is one mind blowing plot twist. It wouldn't cause too many paradoxes because it's obvious that Rory(just like that Professor from Utopia) has no idea what's going on. He maybe has a vague idea that something's not quite right (he doesn't even blink when he walks into TARDIS for the first time), but as the time progresses and Rory becomes more bad ass, The Master starts to reawake. Maybe we'll say goodbye to Rory Pond in New York, but see the Master again in the series finale.
Okay, I'm not here to disparage anyone's Draco in Leather Pants fantasies (that's a technical term; cf TVTropes). But applying actual canon to the theory, you can put those pieces into a much simpler picture than a conspiracy theory. (And I'm fond of Occam's Razor.) I've seen the video that proposes this theory, and been through it point by point on my blog; you can read it here.
If you're in a TL;DR mood, here are my responses to your arguments: "In Let's Kill Hitler," the fact that Rory's head is "banging" instead of exploding after being "exposed to RAW TIME ENERGY" is a testament to how tough he's become as the Last Centurion. (Also, Amy is making a joke there.) In "The God Complex," the fact that Rory has no room is also because he's spent two thousand years as a plastic Roman protecting his beloved from every conceivable danger (including the goddamn Blitz) and so nothing scares him anymore. And in the Doctor's room, it could've been anybody. Possibly the Master. Possibly the Valeyard (who is basically an evil twelfth Doctor), and given Moffat's love of continuity references I suggest that the Doctor's biggest fear is becoming the Valeyard. As for the cloister bell (that alarm noise), it has also sounded in the Children in Need special "Time Crash" (no Master there, and that's the story where the New Series learns what the sound is) not to mention at the Doctor's regeneration in "Logopolis" (no Master, just a difficult death). And a couple of other places, not associated with the Master, but rather with anything post-Fourth-Doctor that threatens the destruction of the TARDIS.
So there you go. Moffat doesn't have to be scared of making any twist he wants (and we know he isn't) for this to make sense. Rory's just a Badass Normal.
To Neira: He blew our minds with River Song; he doesn't need to fabricate the Master out of a really nice guy. And we already know Arthur Darvill is done filming. And it's not the Time Lords; Time Lords are gone, Time War was RTD's idea and Moffat's moved on in the story. That was all the work of the Silence, and given the nature of the Silence, they can't be manipulated. Perhaps they even manipulated the Time Lords, but Moffat will never tell us that.
Yeah, you're probably right. I know Moffat likes the idea of the Doctor being the last of his kind. With Rory being the Master two perfectly good series full of character development turn useless. It's a good idea for fanfiction.
But you have to admit one thing: In the next series or two, we will find out something big about Doctor, something that has been haunting him his whole live. Doctor Who? It's not his name, but his identity. I've read a lot of theories, from that he is actually the Master to him being the creator of humans(that would explain his fascination with modern day UK). Who knows the most about his past? His own people who he, for all intents and purposes, killed.
On the other hand, I suck at making fan theories. I couldn't have figure out who River Song was if Moffat spelled it out for me. I have a bigger chance of guessing how Sherlock survived the fall then being anywhere near the right plot twist.
There was all kinds of Classic-era fanwank. The bit in Series 3 where Martha asks whether the Doctor and the Master are brothers, and the Doctor replies "You watch too much television", exists to debunk the theory that the Doctor was either the Master or his brother, which was popular before the show went off the air in the 80s.
And really, what can we learn about the Doctor that's bigger than "Amy's Choice"? "Physician, heal thyself" is complete bullshit.
As for fan theories, I could tell you a way Sherlock could have survived which fits in with everything I know about Moffat, and how about you tell me how off it sounds?
In the original series for the kids (which I was when I first watched) you couldn't quite tell if they were supposed to be father and son or son and father. It is only the recent series that suggested that they were the equivalent of boarding school mates. No one had suggested to me as a teen that perhaps they were intimately involved at one point, the only slash out there at the time being "Kirk/Spock" which was kind of a squick for an inexperienced straight teen girl.
Father and son? Hmm...I haven't gotten to Three yet, in my quest to watch it all in order, but I'll have to look for the Darth Vader dynamic when I get there.
And have you accepted Kirk/Spock yet? *evil grin*
Wow! I never thought of that! But that still is a viable theory!
When is Season 7 out in the UK, then in the US?
September, I think. And it'll air the same day in the UK as in the US, or so I've heard.
And no, it is no longer a viable theory; it was denied by a more honest Doctor than the current one.
What do you mean, a 'more honest Doctor'?
And thanks for the release date.
More honest than Eleven. It was Ten who denied that he and the Master were related.
Wait, I didn't mean the related thing.
Then what did you mean? The theory that Rory and the Master are the same person? That was never a viable theory, and if you care to scroll up, I devoted a lot of time and energy to taking it apart.