This is a theory that probably will never be proved or disproved. It’s unlikely Rory will ever return to Doctor Who, however it’s very plausible that he is the Master. Although we the audience don’t know it, and Rory himself didn’t know it, there are several reasons to believe that he is in fact the Doctor’s Time Lord counterpart.
Yes this is a very outlandish theory but bear with me. Firstly and most obviously, throughout his time as a companion, Rory had a habit of dying and then reappearing. Steven Moffat never really explained how Rory survived being consumed by the crack in “Cold Blood”, other than saying sometimes miracles do happen. He also returns as an Auton of the Nestene Conciousness. Interesting, as the Master first appeared in “Terror of the Autons” back in Jon Pertwee’s era, where the Master did work with the Autons. It would also go some way to explaining how he went through 2000 years protecting the Pandorica without damaging his body. Surely it is beyond the basic survival instinct of a human to survive without a scratch for that long? The Master is an expert at clinging on to life and he would have had the expertise to survive the crack and return as an Auton, whereas we were never offered a concrete explanation as to how Rory managed it. Now although Rory wasn’t aware he was the Master, if he was concealed by a chameleon circuit and a fob watch that we saw hide Derek Jacobi’s Master in Utopia, he would’ve still shared some traits with his Time Lord self. Professor Yana was still extraordinarily clever, so Rory could’ve perceivably managed to return made of plastic.
The next bit of evidence that Rory could be the Master is the presence of a fob watch in “The Power of Three”. As you can see in the above image, there is a fob watch in Rory and Amy’s house. This seems like a strange prop to be randomly placed on a table, especially with its relevance in the show’s history. This fob watch is where a Time Lord’s biology and D.N.A. is stored when he temporarily changes to be human. Fob watches aren’t common nowadays in Rory and Amy’s time, so why do they own one? Coincidence? Maybe, but it’s another piece of the puzzle that all seems to fit nicely together.
An even stronger bit of evidence comes back in series five in “The Vampires of Venice”. Rory is taking his first trip in the TARDIS and acts completely normal and almost oblivious to the fact that it is bigger on the inside. It’s almost traditional for companions, especially in the modern era, to be initially astounded by the size of the ship’s interior, but Rory is completely nonplussed. When the Doctor mentions that it is a lot to take in, Rory calmly explains how he knows that there’s an extra dimension and that he isn’t surprised at all because he’s been reading up on it. There’s reading up on something and then there’s this. Surely a bit of reading couldn’t prepare someone for one of the greatest miracles they’ll ever see? So this would suggest that Rory is no stranger to Time Lord science such as that of the TARDIS. Although he won’t fully remember why, the concept won’t be fully alien to him and that could be why he acted as if he was simply riding on a bus.
Now onto another one of Moffat’s more dubious plots. Although the reveal of River Song as Rory and Amy’s daughter was brilliant, is the theory that she has Time Lord genes just because she was conceived in the time vortex really that plausible? As explained when River is kidnapped, it’s very difficult to create a Time Lord, so surely two humans couldn’t accidentally just happen to do it, in the time vortex or not. If Rory was the Master then it would certainly clear up why River is part Time Lord.
Finally, the most compelling piece of evidence came in “Let’s Kill Hitler”. Just after Mel regenerated into River and Rory was exposed to all of that regeneration energy, he rather randomly announced that he was “getting this kind of banging” in his head. John Simm’s Master was prone to a constant drum beat in his head, planted there by the Time Lords so that they could return. Could this be the same noise? It seems like a very odd thing to say. Surely a normal person would say “headache”? The exact use of the word “banging” is just so precise and certainly makes it possible that it was the same banging experienced by Professor Yana and Simm’s Master.
So yes there are several counter arguments to all the above points. Rory’s story is finished? Yes it is, but that doesn’t mean he couldn’t be the Master. He’s had several bodies so if he was disguised as a human, the Master could easily go and get another body once Rory eventually dies. Rory Williams could be unsuspecting of not being human his whole life, just like Professor Yana. Why did Moffat never reveal that he was the Master if he planned all of that? Well yes, you would expect such a maticulously detailed and crafty plan to be followed through until it reached its ending, but Steven Moffat is not like any other writer. He is the king of the tease, he loves poking fans with potential twists and developments but not actually going by what he suggested. It could all be a bit of a game by Moffat. Who knows? Once his tenure as show runner is over, he may reveal that Rory was always the Master. What incarnation of the Master could Rory be? Rory could be almost any unknown incarnation. There’s nothing that suggests he couldn’t be a pre Roger Delgado version, making him the earliest known Master. There still hasn’t been a link between John Simm and Michelle Gomez’s incarnations. If the Master needed a route back to Earth after “The End of Time” then maybe Rory was that link.
Overall, I think this theory has a lot more substance than most others. Although I wouldn’t be comfortable putting a lot of money on it being true, I certainly wouldn’t rule it out. Arthur Darvill is certainly young enough to return to the show even 10-15 years down the line, even if another writer wanted to pick this tantalising lead up. If we never hear any more about it, it still can’t be ruled out. Doctor Who has a strange habit of throwing up the most unexpected plot twists. We went eight years without knowing there was another incarnation of the Doctor between McGann and Ecclestone. So would it really be so surprising if we were to find out that the Doctor had been unknowingly travelling with The Master as his companion?