This idea came to me while watching "The Rise of Chaos", and I just had to get it down. It was a lot of fun to write; I love both shows, and I've been wanting a Doctor Who plot bunny to come to me for a while. So, here it is!
Disclaimer: Don't own anything recognizable.
Flynn stared the... thing down. Whatever it was - and it definitely wasn't an alien, whatever Ezekiel thought - glared right back, unmoved.
Deciding the staring contest wasn't getting him any closer to the artifact, Flynn straightened his shoulders, took a deep breath, and changed tactics.
"Do you know who I am?" He asked, standing as threateningly as he could, which was hard without Eve. Eve did the whole scary thing a lot better than he did.
"No," the thing replied, unimpressed.
"You should," Flynn continued. "Because I" he dramatically pointed to himself, "have defeated many villains. I have defeated foes that would send you crawling back to your mommy. I save the world almost every day! So don't tell me that you haven't heard of me - everyone has heard of me! So, let me ask you again, do you know who I am?"
The thing looked impressed - finally - but what it said next didn't make any sense. "The Doctor?"
Flynn blinked. "Who?"
The Doctor threateningly adjusted his bow tie as he stared his foe down. Whoever she was, she was from Earth, but she had access to technology The Doctor had never seen before.
And no, it wasn't magic, no matter what Rory said.
"Do you know who I am?" He asked, lowering his voice. He stared into the woman's eyes with such intensity it should have melted her.
She held his gaze and snarled. "No."
"Well, you should. Because I have faced species you couldn't dream up. I have saved this planet more times than you have blinked. And trust me when I say that this planet is under my protection. Now, tell me, do you know who I am?"
The woman hissed. "The librarian."
The Doctor blinked. "Who?"
"Have you ever heard of the Doctor?"
Jenkins looked up from his desk with raised eyebrows, telling Flynn that he did recognize the... title? Name? Eve and the other librarians also stayed, despite the debriefing being finished.
"The Doctor?" Eve repeated. "Where did you hear that?"
"Alien," Ezekiel interrupted.
"No," Flynn replied, gesturing dramatically to emphasize the word. "There is no such thing as aliens."
"Actually, sir," Jenkins intervened. "I wouldn't be so sure. Did the... thing, for lack of better words, assume you were someone called The Doctor?"
"You've heard of this... doctor person?" Eve asked.
"Yes," Jenkins replied. "Us immortals run into each other often. Though he probably doesn't know much about the library, if anything. He couldn't recognize magic if it landed on his doorway and stole all his scarves."
"He's immortal?" Cassandra asked.
"Yes. Well, sorta. Not technically," Jenkins answered.
"Then what is he?" Eve asked.
"Just very long lived." Jenkins answered.
"A very long lived what?" Jacob asked.
"A very long lived -" Jenkins replied. "And, I apologize in advance, Colonel, because you're not going to like this - time traveling alien."
"What?" Jacob and Flynn yelled at the same time.
"Did you just say 'time traveling alien'?" Eve demanded.
"No, no," Flynn replied. "Aliens don't exist."
"Why not?" Ezekiel asked. "Magic does. Why can't aliens exist?"
"Because..." Jacob started, clearly struggling for a response.
"Statistically," Cassandra said. "Aliens are actually very probable. I mean, the universe is huge, with an infinite number of stars, many with planets orbiting around them. With so many planets, it would be likely that at least some of them were fit for life, and that at least one other actually managed to form life. There being no other planet in the universe with life... well, that's just not very likely."
"Not to mention that not all alien life requires a planet like Earth," Jenkins added.
"But a time traveling alien?" Eve asked. "You know what, that's it. First it was magic, then just regular time travel, and then those ridiculous self-fulfilling prophecies, and now aliens that can time travel. I can't handle this. I'm out."
"And you've never heard of this librarian?" Amy asked in that tone of voice that almost made The Doctor feel like an idiot. It was one of the traits that made a good companion.
"No," The Doctor replied. "Which is why this is bothering me so much. How could someone with so much recognition slip under my notice?"
"Magic?" Rory suggested.
"There is no such thing as magic," The Doctor repeated, for the millionth time that day. "Why can't you get through your head?"
"I don't know," Rory answered. "Maybe because after fighting fish vampires, plastic Roman centurions, and trash cans with plumbers on them, magic doesn't seem so unreasonable."
The Doctor hesitated. Rory did have a point. But, no, he was probably the most experienced person in the universe. If magic existed, he'd know it.
He shook the thought out of his head, and set course for the next adventure.
"Books are the best weapons in the world" - The Doctor