Before you go screaming, this isn't official or anything but everything just adds up. If you don't want anything spoiled, I advise you cease reading this blog now.
- Spoilers Ahead -
While a lot of people think this is extremely ridiculous, I believe it is true. At first I couldn't believe it, but impending evidence brought me to think otherwise. Upon re-watching clips, I noticed some evidence myself, as well. This would be one highly dramatic plot point and I think it would make more than enough sense to implement into the storyline.
Rory's daughter (River Song/Melody Pond) is a Time Lord and is supposedly this way because of exposure to the TARDIS. While this sounds like a good enough explanation, it doesn't make too much sense. If Rory were a Time Lord it would be plenty relevant enough for his own daughter to be a Time Lord as well. And no- this isn't my evidence its just to get my point across.
Rory was originally just some guy but he significantly grew into a much more important character. As time progressed, his personality changed significantly, too. I'm sure plenty of you have noticed Rory's aggressive reactions in later episodes. I'd also like to point out that Rory is the only human with no indication of surprise once seeing the TARDIS was bigger on the inside.
Now let's pull you back to the episode know as The God Complex. It seems to get its point across, but I think it is much more than it seems. The episode is being debated constantly, if you hadn't noticed. The most debated part is the Doctor's room (Room #11) which remains unexplained. Due to the Doctor's fear of himself and his quote, many believe he saw himself. However, we also hear the TARDIS' Cloister Bell (Distress Signal) which has only been heard once before when the Master turned it into the Paradox Machine. Please note that the Cloister Bell sounds a total of four times, which could also be a reference to the Master.
In this episode, there was also a scene between the various characters where the Doctor was discussing the rooms and how they worked. He used Rory as an example and pointed out that Rory had no faiths, religion and was not at all superstitious. While I can understand the fact that he has no religion, I want to know how he can't have any sort of faith. You'd at least think he'd believe in his wife or at least try and deny it in front of her.
Later in the episode, Rory talks in the past tense as if he had traveled with the Doctor many times before. "Well, after all the time I spent with you in the TARDIS, what was left to be scared of?" I believe this is a response to the above, but it is beyond strange how he talks like this. After the Doctor says something about it, he denies it and they go on with the episode. BUT WAIT. After re-watching this clip, I happened to hear something that sounded like four heartbeats (Maybe even drums) in the background. It could have been some kind of error with the audio of the video, but I doubt it. It seemed deliberate to me.
In an earlier episode, Let's Kill Hitler, Rory and Amy witness their childhood friend become River Song. Immediately afterward Rory says that he's feeling a 'Sort of banging in his head,' but Amy brushes it off with a joke ("Probably just Hitler in the cupboard.") and everyone just ignores it. Though he could have been confused/stunned/stressed, it is quite odd that it happens just as quick as it is brushed away. If he were a Time Lord with no memory of his past form, raw time energy like this would cause subliminal issues within his conscious leading to the banging. Please note that there is never any 'banging' noise when Rory states this.
Another thing would be the little detail into Rory's past. For all we know, he could be adopted or not have parents at all (But that would be suspicious). Although we know that he's been Amy's friend since he was a child we have no clue where he came from. Some people deny the possibility of him regenerating into a child, but its possible as demonstrated by River.
Now imagine this- Rory > Yana > Saxon
Since the Master's latest incarnation was thrust back to the time war, I find it more likely that he had an incarnation before rather than an incarnation afterward. Perhaps Rory came before Professor Yana and learned of his identity. If this were true, I think he would make up some genius plan to destroy the Doctor and take over the world or something. If this were the case, I imagine him regenerating into a younger Professor Yana somehow and having his mind swept by the Doctor. IDK. This concludes my speculation, I think.