I got inspired by the multiple Rory-is-the-Master stories that have appeared over the last few days. Here's my take.
Disclaimer: If you recognize it, I don't own it.
"Do you have one of these?" The Doctor held up a silver pocket watch. Rory could see the engraved circles and arcs on the closed lid, and the impression of meaning, the sense of being almost-but-not-quite able to read the writing, floated against his mind, tantalizing him, just beyond his grasp.
"I…" he started, tapping his finger against the table surface even faster, one-two-three-four, one-two-three-four, scared by the enormity of the presence he could feel inside his own head that he'd known but never really realized was there. Not until the Doctor had called him out on the tapping.
Sitting next to him, Amy stared into Rory's face, suddenly seeing him as a stranger. Something other than the boy she'd grown up with. She turned to the Doctor, across the table from them. "What is that watch, Doctor? And what do you mean, Rory's not real?"
"Physically, it's just a fob watch. But what it can hold is so, so much more." The Doctor was still staring at Rory, studying his face, full of wariness and sympathy and resignation and hope.
"I have a watch like that," admitted Rory. "It's in my stuff. It's kind of a lucky charm, I've always had it. If I keep it safe, then I know I'll be fine." He paused. "I guess that sounds kind of silly."
"Actually, it's not silly at all," said the Doctor. "And you're more right than you know."
"Okay, seriously, you two," said Amy. "What are you talking about? Explain!"
"The Chameleon Arch," said the Doctor, earning a confused blink from Amy. "It's possible to physically transform one organism into a completely different species. As part of the process, the Arch stores the original physical and psychic imprint into a small object which, when activated, will restore the organism to its original form. In the case of a Time Lord becoming a different species, the object has traditionally been a timepiece of some sort, usually a fob watch like this one." He sighed, looking at the watch in his hand. "I've done it myself, once before. It wasn't pleasant."
"Wait, you're not saying…" Rory trailed off, the gradually increasing volume of the drumbeats now almost drowning out his thoughts.
"I know who you are," whispered the Doctor. "The rhythm of four gave it away."
"You said Rory wasn't real! What did you mean? Who is he, really?" Amy was nearly hysterical and, in the Doctor's estimation, about ready to slap someone, probably him.
"Rory Williams is a fiction, a construct," said the Doctor, edging away from Amy. "His memories and personality are locked away in the watch that he's kept as a lucky charm for all his life, aren't they, Rory?"
Rory was staring blankly at the table in front of him. "All I have to do is open it. I'm right, aren't I? I just have to open it, and I come back? The real me?"
"But you won't be Rory anymore! Will he, Doctor? Would he even love me anymore? Would I love him?"
The Doctor shook his head. "If he were anyone else, you two might have a chance. But I know exactly who you are." He looked up at Rory, sadly. "It's not just your memories that have been locked away. It's your psychosis."
Amy and Rory stared at the Doctor, aghast. "What do you mean, his psychosis?" demanded Amy. "Are you saying he's crazy?"
"Rory, I've known you for a while," said the Doctor. "You're levelheaded, you're the rock of stability when Amy and I go flying off for adventures. You keep us grounded. It's as if too much of your natural craziness got locked away. He's always been like that, hasn't he, Amy? Even while growing up? The one voice telling the rest of you kids that you shouldn't break into the school grounds after dark, that you shouldn't drink the alcohol that one of you snuck out of your parents' liquor cabinet, that you shouldn't go vandalizing or whatever you youngsters get up to when there aren't any adults looking?"
"Well," said Amy doubtfully. "Compared to Mels, anyone would seem like that."
The Doctor hesitated. "Point taken. But what I'm saying is, Rory wasn't a natural kid. He was created to be the perfect kid, as the perfect disguise, and he stands out because of it."
"Doctor, what happens if I open that watch?" Rory was not interested in the review of his characteristics as a human child – he wanted to know about his future.
"You regain your memories, and your personality… and your body physically changes back to Gallifreyan physiology. That last bit will be rather painful. Your single heart will split into two…."
"And I go mad."
"You always were. Since you were a child. It's just been suppressed."
"And I won't love Amy anymore. Will I?"
The Doctor didn't answer for a moment, thinking of Lucy Saxon. "I don't think you're capable of love," he said. "You can possess people, use them…."
"Then I won't do it."
Both the Doctor and Amy stared at him. "But you're not really…." The Doctor was interrupted by Amy throwing her arms around Rory and kissing him passionately. "Breathe!" said the Doctor. "Honestly, you humans don't have respiratory bypass systems, I don't know how you…"
Amy broke the kiss first. "Do you really mean it?" she asked. "You'd give up your real identity for me?"
"Of course I would!" said Rory. "I can live with the drums in my head, if it means I get to keep you!"
"For what it's worth," said the Doctor, "the drums would get worse if you came back."
"Then I'm definitely staying human," declared Rory. "Doctor, I'll give you that watch, and you can destroy it or hide it away somewhere, I don't care. I'm never opening it. I'd lose too much!" He went back to kissing Amy.
The Doctor smiled, and got up from the table and left the TARDIS kitchen. A tiny piece of him was disappointed that the only other Time Lord would remain gone and he'd still be alone, but considering how much damage the Master always caused with his schemes, and how strong an ally and a friend Rory Williams had proven to be, then perhaps this was for the best. And in the meantime, he knew exactly which ultra-secure TARDIS storeroom he could use to stash that watch….