Doctor Who and Harry Potter. The first being my favourite TV show, the second being my favourite books that I can do a good crossover for. I like the story.
Note: if there are any pairings you want to add, just say. This is one of the things I write more for the story than the pairings. I was thinking about a Harry/Draco (you'll see), but if there are any objections, let me know.
I don't know if I'll continue this or not, it is an odd idea, but I am just generally odd.

The 11th doctor enters Hogwarts. Things go...differently.

"What is it, old girl?" the Doctor crooned softly, running a hand down a pillar as the TARDIS made an odd groaning sound. He brushed his long, tousled hair aside with a finger, to get a clearer sight of the screen. "Can't be anything too big, ooh, temporal flux, been a while since we've had one of those, and it's… Earth, oh it's always Earth, humans," he muttered the name like a curse, before grinning, "Bit like me actually. Oh, bit more detail, good, good-" his mumbled rant stopped as he stared at the screen, before he finished with an appalled "No!"

"That doesn't sound good, Doctor!" Amy called out from one of the side rooms, before skipping out into the console chamber

"It's not," the Doctor shot back, walking around and using his hands to manipulate the console, while keeping his head completely still, eyes fixed on the screen. "Got to land, find the anomaly."

"Where this time?" Amy skipped over to just behind the frantic Time Lord

"Hogwarts," the Doctor replied, pronouncing the word like he expected to be disbelieved

"Huh? Hogwarts as in Harry Potter?" Amy frowned, excited

"No, Hogwarts as in Dirk Gently, of course Harry Potter!"

"That's just fiction…isn't it?"

"Nah," the Doctor shook his head, "Words have power, temporal echoes of our good friend Mr Potter's life fed into JK's mind."

"No way, so we're going to meet Dumbledore?"

"Ah, no, you're not going."

"Come on Doctor!"

"There's a massively, hugely dangerous temporal flux in his first year at Hogwarts, no idea what caused it, but we can't raise suspicion unless we want it to happen again. Not much call for adult Scottish girls in Hogwarts."

"So what're you gonna do?" Amy challenged, crossing her arms and resting them on the console.

"First year, I understand they're missing a teacher," the Doctor grinned, flashing the psychic paper.

O

"Be back in a sec," the Doctor waved, stepping into the TARDIS, "Or a day, you know how things can be," he waved, leaving Amy, and a certain Mr Pond, in a field somewhere. He wasn't completely certain where, not that he'd tell her that.

"Doctor!" Amy ran up, about to bang on the TARDIS door-she hadn't banked on waiting years again. Instead, her hands passed straight through the air as the time machine vanished.

O

"Sorry Quirrell," the Doctor straightened his bow tie, muttering, as he stepped into the daunting castle, sonic screwdriver at his side, contained in a slightly thick, willow wand. He just hoped he'd get the job.

O

The Hogwarts Express. It trundled along the tracks, containing lots of humans, as normal, and one Time Lord.

"I must say," McGonagall remarked, "That is a most interesting wand you carry, Mr…"

"Doctor," he replied, "Willow with, ah, Leadworth core."

"Leadworth?" the Professor frowned

"Yes, it's very…rare, very magic, um, want a cauldron cake?" the Doctor bounced up, trying to escape the conversation as the sweets trolley came by. He reached into a pocket, taking a jangling few coins out, which he'd taken from Gringotts by means of his psychic paper. Before he could buy anything however, Dumbledore walked down the corridor.

"Excuse me," the elderly head-teacher nodded, "I have a matter of grave importance to discuss."

"Headmaster," McGonagall bowed her head slightly to allow the bearded wizard into the compartment.

"Thank you," Dumbledore spoke politely, "You are the first teachers I have told of this. This year, at Hogwarts, we have been charged with the protection of the Philosopher's Stone."

"Headmaster, is that wise? Considering who's starting here, just today-"

"I am well aware of the risks Minerva. However, it is a far greater risk to leave it in the outside world. That is why I am asking all of our teachers to create some form of defence, so no students nor unwanted visitors may find the stone."

That instant, there was a cry as, at the other end of the carriage, one teacher forced a checkmate with another, a Knight staring down a King on a chessboard.

"Headmaster," Minerva began, "Will that be enough?"
"Rest assured, I will add my own, ah, quirks to the proceedings. I hope this will not prove too much of a challenge for our new Defence Against the Dark Arts teacher, Doctor?"

"No, no," the Doctor shook his head, "You don't have to worry Dumbledore," he grinned, "I can think of a few things."
"Good," the headmaster nodded, eyes twinkling at the Doctor's almost infectious happiness, "Now if you'll excuse me, I must talk with the others."

O

The Doctor leant back, flicking through a 56th century edition of Harry Potter and the Philosopher's Stone as the train neared Hogwarts. He had refused to wear robes, and instead was garbed in his normal suit and bow tie.

"I though Professor Quirrell was supposed to be taking this job," a cold, sneering voice alerted the Doctor. He waited a few seconds, flicking through the book and finishing it, before looking up to see Snape.

"Severus, is it?" the Doctor grinned, in contrast to the expression of dislike on the wizard's face. "There was some confusion, old Quirinus forgot he had the job, and moved away. Luckily, you've got me instead!"

"Are you always this…lucky," Snape's nasal tones did nothing to dampen the Doctor's spirits.

"Not often," the Doctor quickly hid his book as Severus moved closer, "But you know what they say"

"No."

"Me neither," the Doctor slumped a little. "You hear who's joining this year? Harry Potter!"

"He is just another student. Give him no special treatment," Snape pronounced the words like they left a bad taste in his mouth.

"Wasn't going t," the Doctor shook his head, "He's got his mother's eyes you know."

"You knew Lily and James Potter?" Snape pursed his lips

"Only by reputation," the Doctor hastily covered his tracks. It wouldn't do to sound too suspicious.

Severus Snape left the carriage, irritated by the Doctor's optimism. Shrugging, the Doctor took out another book from his pocket; the second Harry Potter book. Knowing a little background never hurt; especially when something was disturbing the time streams, centred at where he was heading.

O

"Who's that one?" the young Harry Potter pointed up at the teacher's table.

"That, oh that's-" a red haired Ron frowned, "Hang on, never seen him before."

"That would be the Doctor," a ghost slid out of the wall, "The latest replacement."

"I thought," Harry paused to remember the skittish man in the Leaky Cauldron, "Quirrell was teaching here?"

"Oh, he was," the ghost, Nearly Headless Nick, said, "But he never turned up. The Doctor took his place."

"Who's that one with the long black hair?" Harry frowned again, pointing once more to the table

"That's Snape," Ron whispered, "Blimey, he does look cheesed off, huh?"

"Students!" Minerva McGonagall called the line of first years down the hall, trying to inject some order into the line that went down between two tables full of the older years.

O

"Boot, Terry!"

The Doctor ignored the cry of the professor, as the Sorting Hat continued its task. Instead, the Time Lord was holding his 'wand' beneath the table, clicking the sonic screwdriver within it. Technically electricity shouldn't work here, but he'd changed a couple of settings on the screwdriver to power it with the magic in the air.

The centre of the willow wand shimmered blue, while his trouser legs muffled the buzzing.

It was supposed to detect whatever was causing the temporal anomaly. This wasn't supposed to take that long; not that there was a time limit; he thought briefly of Amy and Rory, before deciding that the TARDIS was behaving, so he could get back seconds after he left them. He hoped.

Still nothing. The Doctor frowned; had he arrived before the temporal flux had begun? Time travel was always confusing.

"Potter, Harry!"

His ears perked up as the name was called: didn't want to miss this. The hat was placed on the youth's head. A long few moments passed, some kind of murmuring occurring around the young wizard.

All the hairs on the back of the Doctor's neck stood on end.

The hat seemed to mull something over quietly after ten or so seconds. Harry seemed to whisper something, and that appeared to be the key. A moment later, the hat declared, "Slytherin!"

Harry Potter, smiling, went over to the surprised, and yet cheering table.

The Doctor blinked: that hadn't happened in the book.