First off, sorry to the none-Whovians who have no clue what I'm babbling about.
Second, let me make this clear: this is still a FAN-THEORY...so far.
But lately, the theory that Rory is really the Master has been becoming more and more prevalent, and I'm honestly on board. Here are my main two arguments:
1. Remember in Let's Kill Hitler when he starts to complain about a banging in his head, and Amy says it's just Hitler in the cupboard?
2. It would explain some of his behavior.
After Mels regenerates into River Song, exposing the Ponds to Time Lord energy for the FIRST TIME, he begins to complain of a banging noise in his head. Amy dismisses it as Hitler (never thought I'd have to say that). Now, my guess is that he used a Chameleon Arch to disguise himself as an average human. But River's regeneration would trigger something in his mind, making the Drums return.
In addition, the first fan-theory came after only ONE episode: his hospital badge, dating back to the early 90's. If the Master disguised himself, not only would the badge have to be slightly outdated, but it'd be forged, and the Master would have no recollection of his past life, like Professor Yana. This would explain his entire "childhood" with Amy, and a set of false memories to boot. AND: if we're including the Pandorica incident, Auton Rory still had regular Rory's memories. Why? Because the Universe is lazy and doesn't bother with anomalies. A robot of a Time Lord disguised as a scrawny human certainly is an anomaly. ALSO: in the episodes following Let's Kill Hitler, Rory's gotten more and more aggressive. The insanity of the drums is returning, and as human Rory realizes something's wrong, he proclaims in The Girl Who Waited "You're turning me into you!" Not only is this a statement about having to choose between Amys, but also the fact that the more he travels with the Doctor, the more he realizes all is not as it seems. (This would also explain his numerous deaths and resurrections: the Time Lord in him keeps him alive, but the human-ness keeps him from regenerating totally, like Jenny) LAST BIT: in The God Complex, the Doctor opens the door to Room 11. This is the episode directly after The Girl Who Waited, where Rory claims he's becoming more and more like the Doctor. He hears the cloister bell to the TARDIS toll four times (something it does only when the Master is around), and he murmurs "Of course." This could mean that the Doctor knows the Master is returning, too. He just doesn't know who, how, when, or where.
I just heard about this theory 30 minutes ago, and I'm already convinced: Rory Pond-Williams is The Master.
EDIT: Ooh! I found a pretty picture! It's catching on!! [link]
AND ANOTHER THING: Every article that I've read that talks about the Ponds leaving has it written as "Amy Pond and Rory" or some variation. Could it be..?