Rory had known the Doctor was alien since the Giant Deadly Alien Eyeballs of Death had declared him "not of this world." It was the little things that made him believe it.
His first morning on the TARDIS, he trailed after Amy to the kitchen, trying to memorize the overly complex sequence of turns and wondering where he could find paper to map this place. He was on a timeship. A time-and-space ship. An incredibly advanced and extremely disconcerting time-and-space ship, piloted by someone Rory hadn't entirely made up his mind about, although he couldn't quite dislike the Doctor after seeing him try to send Amy back to safety–he honestly did care about the people around him, it was just that he didn't seem to register that going alone into enemy territory was really incredibly dangerous and maybe he should think twice before encouraging it–not that Amy actually needed encouragement to get into trouble, but it certainly didn't help . . .
Rory wondered why the ship had to be so huge inside if there weren't any other crew. He wondered if there were supposed to be more people.
He was quite certain that however different the TARDIS was, the kitchen wasn't supposed to look–well, to look like it had been heavily used for eight hours by a certain hyperactive someone who had started several small fires and tossed eggshells over his shoulder when he was done with them. "We," Amy declared, "are going to be using the food machine for a week, aren't we."
The Doctor gave her an indignant look. Rory said, "What?" and edged into the chaos.
"Last time he had a mad food science night," Amy told him, "the kitchen went walkabout."
"I do not have mad food science nights."
"You made chocolate and jalepeño pizza."
"And you ate it. And liked it. Just like the Tarkalian seaweed spaghetti."
Amy snorted. "Not because I'm sane." She plucked something that looked like crystallized ginger off one of the cooling trays on the counter and ate it. "What were you trying to do here, start a confectionary shop?"
"No–" The Doctor swept the tray away from her before she could swipe another free sample. "I thought I would cook something nice for Rory's first morning on the TARDIS. Maybe crepes. Crepes are cool."
"Because you get to set them on fire," Amy said, "on purpose."
"But then," the Doctor went on, as if the accusation were completely beneath his notice, "I found my candy thermometer, which has been missing for, oh, lifetimes. And you lot sleep for hours anyway, so I had plenty of opportunity to test it on some recipes I've never tried before, and mistakes," he waved his hands helplessly, "may have been made."
Amy nodded understandingly. "They never invented Ritalin on your planet, did they?" She picked up something that looked like a squashy chocolate-covered cherry and popped it into her mouth, whole.
"Ritalin," the Doctor said, "increases focus. If I took it, which I shouldn't, and if it worked on me, which it wouldn't, I would spend all day in a mathematical trance–Amy?"
Amy made a small distressed noise and flapped her hands. Her skin was darkening, achieving that startling flush that only natural gingers could manage. Rory moved forward. "Amy, what is it? What's wrong?"
Amy lunged toward the sink, spat the chocolate-covered whatever-it-was into the basin, and cupped her hands under the tap for a drink–which, in her haste, she slopped everywhere. Then she made a much louder, distressed noise. "Hot–"
The Doctor was already moving toward what Rory assumed to be a fridge. Rory reached it just as he opened it, grabbed the nearest thing that looked like dairy–at least, he assumed that Sauer Creem was a futuristic variant spelling and not false advertising–and thrust the can at Amy.
Amy took a giant mouthful and stopped edging toward purple, although there were still tears running down her cheeks. She breathed deeply, contorted her face, and took another soothing dollop of the cream. "Uggh."
"Sorry," the Doctor said. "I thought covering them with milk chocolate would cancel the effect. They really taste quite sweet otherwise–"
"They taste," Amy said hoarsely, "like pain and burning."
The Doctor picked up one of the deadly chocolates and bit into it. Whatever was inside, it was orange, and he didn't seem bothered by it at all. "That," he said authoritatively, "is not strictly taste. Your nerves–"
"Doctor," Rory said, "what are they?"
"Chocolate-covered Scotch bonnets. They're a pepper that looks like a Tam o' Shanter." The expression and gooey delighted tone that accompanied this information was better suited to a six-year-old girl waking up on her birthday to find a pony. Maybe two ponies. "Tam o' Shanters," the Doctor informed Rory, "are cool."
"Meanwhile," Rory said, "Scotch bonnets are about a million Scoville units of not cool." And the Doctor was currently nibbling on one without a trace of reaction.
Not of this world. Mammals–earth mammals, anyway–all tasted hot peppers, didn't they? But birds didn't, and probably reptiles didn't.
"You," Rory began, "can't actually . . ."
"Taste the capsaicin?" The Doctor grimaced. "That's the problem. I can taste it. I can taste most chemicals, in fact; plenty of things that poison a Time Lord, not as many that can sneak up on me. But the thing is, I taste it as a taste, not a–" He groped physically for the right word. "A fwoomph."
Time Lord. Asking all the questions in his head, Rory decided, was not the priority. "Are you all right?" he said to Amy.
Amy nodded. "Those," she said, pointing at the Scotch bonnets, "go right in the Hazmat biscuit tin."
The Doctor grimaced, but swept up the chocolates. "I honestly thought the milk was supposed to–" Waving hands. "De-hot-ify them."
"There is not enough milk," Amy opined, "in all the milk chocolate in the solar system." She took a last fingerful of sour cream.
Rory looked from Amy to the Doctor. "You have a Hazmat biscuit tin?"