It's weird for me to write this ship since Amy/Rory is one of the few canon ships I like. But I was thinking about what a long time 2,000 years is to spend waiting alone.
London 1910
"You're telling me you've been celibate for almost 2,000 years?" the man asked incredulously.
"Basically. I'm also a virgin," the Roman replied taking another gulp of his beer, "Neither me nor the original, human Rory ever actually slept with Amy."
"Why not take the night off? I can show you a good time," the man smiled winningly.
"I promised I would watch over her," the smaller man worried.
"She's stuck in a magic box; I doubt she'll even notice you're gone."
"At least tell me your name."
"Captain Jack Harkness." The grin he gave Rory then was one that had broken thousands of hearts.
}o{
"I'd forgotten what fun Nestenes can be," Jack joked, "I'll be seeing you again?"
"That depends…"
"On what?"
"You know the Doctor. Would you put him before me? Would you leave me alone in order to follow him?" Jack had to consider for a moment. Usually he would have immediately say that, yes, the Doctor came first. But usually, Jack Harkness didn't ask men he'd just met at a bar if he could see them again. Admittedly, the Doctor was fun, possibly Jack's only chance at a cure and Jack had harboured an unrequited crush on the man for quite a while. But he saw Rory's face – the face of another immortal, a face he could easily see himself falling in love with mutually – and he saw the fear on that face. A fear he knew. Fear of abandonment, of being the second choice, of waiting for someone who would never fully love you back.
The Doctor would always leave Jack. Rory would always stay.
"No. I'd stay with you."
"Then you can visit as much as you like," Rory was adorable with that smirk on his face and Jack told him so before he left.
}o{
June 26, 2010
"Do you ever feel like you've forgotten something really important?" Amy's nervous voice came through his phone. When Rory thought about it there was something nagging the corners of his mind. A man with cocky grin, whose feelings were only for him, no Raggedy Man. "Do you feel like there's a great big thing in your head and you feel like you should remember it but you can't?" she continued. Yes. A man who sent shivers down his spines with a mere look and made him feel more than Amy ever had.
"Yep," he agreed worried about where his thoughts were going. The idea of this man was crazy. He had only ever loved Amy. He wondered if long lasting imaginary "friends" were a trait he and his fiancée shared. Then Amy gave him a way out of these thoughts, apparently his voice hadn't been convincing enough, "Are you just saying yes cos you're scared of me?"
"Yep," he agreed, hoping to banish the insanity with words.
"I love you."
"Yep," he hoped she did, than realized he hadn't replied in kind, "I mean, I love you too." But he didn't, not really, not as much as he loved the man who he had never thought of before today. The man he felt he knew better than Amy, better than himself.
}o{
"It's the Doctor. How did you forget the Doctor! And how did I forget Jack," he murmured the last, wondering if the man even knew him in this world, or if he too had forgotten their one hundred years together.
Rory managed to stay calm and act normally throughout the wedding, which went about as well as any party with the Doctor could, but finally, at the end of the wedding, when the Doctor invited them to travel with him Rory spoke up, "I need to see someone first."
"Who?" Amy's brow furrowed as she tried to think of anyone Rory would need to speak to. Rory didn't answer her. Instead he turned to the Doctor, "Can you take me to Torchwood Three, in Cardiff?" he requested.
"You know people in Torchwood?" the Doctor questioned.
"Wait what's Torchwood?" Amy interrupted.
"A group of humans on Earth who protect against aliens. So I repeat how dose Rory know them?"
"Not them, him. 2,000 years is a long time. Someone noticed."
2006
The team of Torchwood Three looked up as Jack entered, a much smaller man on his arm, "So this is the infamous Torchwood," the man said.
"Yup," Jack agreed, "Rory, meet Ianto, Tosh, Owen and Gwen; guys meet Rory."
Everyone said hi except Owen, "Who exactly is Rory?"
"My husband."
"What?" Gwen exclaimed.
"How long have you been married for?" Tosh questioned.
"About," Jack checked his watch, "six hours."
"Tell me you did not just get drunk and marry this poor man!" Tosh demanded.
"He didn't," Rory defended, "we've been together for a while."
"Why've we never heard of you?" Gwen asked.
"My private life deserves to be just that. Rory was none of your business," Jack answered.
"Was?"
"His old job finished. He's going to work at Torchwood now."
"Are you sure that's a good idea?" Owen eyed Rory, "Bit scrawny isn't he?"
"I've been around a while. I've learnt some things, I don't think you need to worry but me," Rory interjected.
It took Torchwood some time to accept Rory, but they learnt he was stronger than he looked and had a veritable lexicon of alien knowledge as well as being an adept fighter. It helped that although Jack was obviously in love with the boy when they were safe and in private it never interfered with the job. He didn't do crazy things to protect Rory above the others. He was able to trust the man's abilities and control his concern.
"Who would have thought," Jack mused, "The two of us, settled down, working together. Me all calm and relaxed. With a schedule and vacations and everything."
"As a kid I never imagined my job would be fighting aliens. I was going to be a doctor; work my way up. I was a nurse when the Doctor came. Running into my life and turning everything upside down."
"But look on the bright side, that's what brought us together. Meeting the Doctor, becoming immortal," Jack kissed Rory gently, "Now we have an eternity together."
On a TARDIS far away a girl named Melody Pond was born. The Doctor and Amy's Time Lady daughter.
The date they arrive at Torchwood is a made up date after Gwen joins and before the end of season 2 (I have no idea when the series takes place). I haven't seen most of season 6 so sorry if I disregard something from it. And of course I couldn't bear to erase River, though she is the Doctor's daughter rather than wife. I may write a sequel with m-preg if there is interest.