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Rory didn't think that the Raggedy Doctor was real.
In fact, he helped make up the term “the Raggedy Doctor,” after “the Tattered-Clothes Doctor” sounded too offensive and “the Shabby Doctor” too silly. He thought the Doctor was a fantastic character in a great story, like Harry Potter. Then as time went on, the Raggedy Doctor became more important than Harry Potter, to the point where Amy and Rory talked about him all the time, making up secret codes and languages in case any aliens or classmates were listening in.
It was a fun game, which is why they kept it up long after they were “supposed to” abandon such childish pursuits. Amy and Rory would run all around, having adventures and exploring the world together. They found amazing places – parks, museums, even an old phone booth would do for an adventure with the Doctor. All they needed were some outfits, weird food, and their imaginations. Sometimes they alternated who was the Raggedy Doctor and who was the dashing companion. Rory wasn't sure which role he liked better.
As the years went on and puberty set in, their game changed some, but Amy and Rory still loved it. They didn't mind keeping up their childhood game a little longer. And, Rory thought later, it gave them a great excuse to see each other. An excuse for them to be alone, because Amy didn't tell anyone else for years – not until the very end of secondary school. Before then, the Doctor was something that just the two of them shared.
Once, when she was 12 and he was 13, she walked in on him changing out of a pair of raggedy trousers. He blushed then, but didn't really mind, even when she didn't look away – because she was Amy, and she was different.
~
They grew up, and somewhere around the ages of 15 and 16 their mutual love for the Doctor dropped off some. Amy had become, well, gorgeous by then, and took the opportunity to date some of the boys who'd once teased her for her fairy-tale name and made her a bit of a social outcast. She saw a different one every other month, and Rory gradually drifted out of her life. He was still in some of her classes at school, but he hardly hung out with her anymore.
Every now and then, he thought of the Raggedy Doctor again. Sometimes he thought it would be nice if he could travel, really travel through the universe the way Amy's childhood imaginary friend could. He thought he'd like to see the Doctor, if he were real.
At her 17th birthday party, which he thought he was lucky to have been invited to, she told him she'd been an idiot and apologized, and their best-friendship picked up right where it had left off. They went ice-skating and watched the Harry Potter movies and prepped for tests together. She helped him with history, and he helped her with science.
When he asked her out, she didn't quite understand that he wanted to be more than friends. When she realized what he meant, she asked for a week to think about it. Two days later, she came to him after class, wearing a threadbare scarf and an old skirt and whispering, “Yes.”
Rory kissed her for the first time while they were sitting on her bed studying for A-levels, alone in the house she grew up in. Amy kissed him back, and it was only an hour later that they broke away and went back to reviewing the material.
When the tests were over, she suggested they should go on another Raggedy Doctor adventure.
This time, their game was a rather different kind of fantasy.
~
When he found out the Doctor really existed, Rory's mind was blown.
Of course, he'd already been through quite a bit of confusion and disbelief when he found out that his patients, coma patients, had been walking about on the streets of Leadworth. He even managed to talk to one of them, a woman who'd been unconscious for three years, who told him she was going on vacation soon and her life had never been better, before walking away, murmuring about silence.
The appearance of the Raggedy Doctor, clothes tattered and burnt but body unharmed, just took compounded the impossibility of the situation. There was no one else he could be; he looked like one of Amy's childhood pictures, just cleaned up a bit around the edges and shaded in. And so many of his actions were wild and erratic, Rory could easily imagine him as a man – or an alien – who enjoyed the taste of fish custard. He almost asked where the little blue box had been parked. (Amy later told him her backyard.)
The fact that the story of the Raggedy Doctor they'd been talking about for nearly a decade wasn't just a story was the final bit, though. Either Rory had gone mad, or the entire universe had.
After some careful consideration, Rory decided on the rest of the universe. After all, that many people couldn't all hallucinate the sun being obscured by a force field, and the spaceship headed by an enormous blue eye didn't conform to any rational cosmos Rory had ever heard of.
He watched the Doctor and Amy, half in awe and half jealous that she had been right and known him for all those years and he hadn't. They had such a quick chemistry between them. The Doctor's mind worked so fast and she was running alongside him to catch up; Rory just looked on from behind.
After the TARDIS disappeared, Rory was certain that the Doctor was real and they hadn't seen the last of him. Still, Amy was heartbroken, and Rory was left to pull her back together. Six months later, she started smiling again. They stopped talking about the Raggedy Doctor. And a year to the date of the encounter with Prisoner Zero and the Atraxi at the hospital, Rory got down on his knee and asked Amy Pond to marry him.
Rory delved into research on the outer fringes of science, complicated material which he knew the Doctor would have known off the top of his head. Through books and the Internet, he investigated how one creature could steal other being's shapes, how time-travel could work, how a crack in Amy's wall could lead to another world. He studied theories about faster-than-light travel, about black holes, about string theory and the potential for life in other galaxies. When the Doctor came back, he wanted to be ready.
~
He hadn't studied enough.
The possibility that Amy had fallen in love with the Doctor had of course gone through Rory's mind several times. But he was a madman from across the universe, a solitary wanderer, and besides, he had left her. The fact that her crush might've been requited had never once seriously entered his head.
She'd snogged him. He'd run off with her. They'd gone away together the night before the wedding.
He'd never seen Amy as the runaway bride type, the kind to get cold feet and flee, but then he couldn't envision her falling for any other man besides the Doctor. And that was a battle Rory had already lost.
Perhaps Amy had never really thought of them when they kissed, or when he wove his hands through her ginger hair and told her “I love you.”
Maybe all those years he had just been a substitute.
~
Rory didn't like the Doctor at all in Venice.
He was gangly and impossible and fascinated by things that weren't right, even if he couldn't set them right. He moved too fast, and was too dangerous. He made Amy do tremendously foolish things, and Rory felt the desire to prove himself the same way that he knew she must have. He knew then that they would never really be safe around the Doctor.
Then somehow, miraculously, he saved them. Rory, Amy, the Venetians, all of them ended up fine. True, if it hadn't been for the Doctor then the vampire girls and the explosives merchant and Signora Calvierri and her son wouldn't be dead, but if the Doctor hadn't been real then Venice would've been flooded and lost. Rory had some Italian blood on one side of his family, a couple of great-grandparents. Perhaps he'd saved his ancestors. Perhaps otherwise Rory would've been erased from time.
And Amy walked back into the TARDIS triumphant, and called them “her boys.” For the moment, he was just glad he was still one of her boys, considering the other boy in that equation.
It would take him a while to figure out where he fit into this arrangement. Rory could live with that.
~
Rory didn't know when his life became so complicated, but he knew it was Amy's fault. And he knew complicated didn't matter nearly as much as loving Amy. As long as she was by his side, he was happy. The universe was vast, and the rest could be worked out later.