Ok, go back about a month when I first found out about this crazy theory that people have when a friend showed me a small part of a discussion online. I didn't think it was at all possible but I looked around and watched the episodes with Rory and the Master again and the more I look into it the more likely it seems. This isn't a story per se but I hope it'll be ok.
If you notice in The God Complex, the Doctor says "Of course, who else?" not "Of course, what else?" when he looks into the room that holds his greatest fear. Then you hear the TARDIS distress signal that you pretty much only hear when the Master is messing with the TARDIS or something. Many people would think that the daleks are the Doctor's greatest fear, but they may not be because they are described as his greatest enemy. A part that proves it even more is in Let's Kill Hitler. After they see Mels regenerate, he says "I'm getting this sort of banging in my head." It's dismissed when Amy just says that it's just Hitler in the cupboard. They did not give you enough time to really think about it.
In The God Complex Rory speaks in past tense and the Doctor comments on it. In The Doctor's Wife, Idris kept messing up the tenses. I would make sense for a time traveler to mess something like that up because nothing is ever really the present for them, especially for the Master and the Doctor because they do not exactly have a home because Gallifrey was destroyed. Rory showed no sign of surprise when he saw that the TARDIS was bigger on the inside. There probably was not anyone that knew about the TARDIS that would write about it online or in the books because pretty much only his companions knew that and they would most likely try to keep the secret, even after they stopped traveling with the Doctor. Therefore, the only way that comes to mind that Rory would not be surprised is that he has been in the TARDIS before. It would explain River's timelord DNA better. She could've gotten it from Rory instead of somehow from the TARDIS.
Another theory I have is that when Rory died for the first time in Cold Blood (took the shot for the Doctor); he was consumed by the crack in wall and might've been gone for good. A few episodes later, in The Pandorica Opens, when Rory comes back it's not really Rory but in fact the Master who had taken the shape of Rory. So really Rory was gone forever and they just assumed that it was the real Rory, since they were so overjoyed that he was back. The Master could've realized what their reactions would be because he went through Amy or the Doctor's memory like the group of aliens did with the Pandorica/ Pandora's Box, the Romans from the book and Rory.
I know it's really jumbled but I wanted to get the words down. Let me know what you think.
R&R
~iggsplosives