Full Summary: After losing Amy and Rory to the Weeping Angels, The Doctor decided to retire. The Tardis, however, had other plans for her thief. Now, he has a teaching position at 1991 Hogwarts, and has a energetic and inquisitive 11 year old girl in tow who calls him "dad". Will the Doctor be able to successful manage to teach a bunch of wizards and witches Muggle Studies, the proper and unbiased way? And will his 'daughter' and her friends stay out of trouble? And most importantly, will the Doctor accept his fate of being a father again? Or will he break both his hearts again by leaving her behind?

A/N: Might want to grab a tissue box. This first chapter will contain lots of feels.

Chapter One

Two Lonely Souls

Why? Why did that Angel take away his Amy and Rory? His beloved Ponds? His best friends? His- dare he say it- in-laws?

He had managed to save Amy and Rory from the Weeping Angels, save all of Manhattan. But one angel got through. One angel survived. And now he will forever hate that angel.

It had taken Rory first. They were on their way back to the Tardis, parked in the graveyard. Rory had called Amy's name, then he was gone. Just like that. In his place was a Weeping Angel, pointing its finger at the gravestone Rory had been staring at mere seconds ago. Engraved in the stone were the words:

In Loving Memory

Rory Arthur Williams

Aged 82

Amy, of course, was devastated. She asked, no begged the Doctor to go back and save Rory. But it was impossible. Going back meant destroying all of New York. Even though he also wanted to save Rory, the Doctor knew he couldn't risk the millions of lives in the city. So instead of going on with the Doctor, she decided to join her husband.

And so the Angel had taken Amy from him.

And words were added to the gravestone:

And his loving wife

Amelia Williams

Aged 87

No longer will he trip over things the Ponds left lying around. No longer will he share adventures with his best friends. No more Amy. No more Rory. No more raggedy man.

No more Doctor.

He couldn't do this any longer. Both his hearts had been broken to many times. Now, they were shattered. And he doubted anyone could ever fix them.

Amy told River to stay with him. But she didn't. She left, and the Doctor knew the fate that awaited her. And that, too, broke his hearts.

Victoria London, a nice place to retire the Doctor thought to himself, messing around with the controls, but not with his usual energy. Madam Vastra, Jenny Flint, and Strax were there too. A least he'll have a little company.

The Tardis landed with a soft thump, but the Doctor stood at the controls awhile longer, fingering a lever. Sadness still overwhelmed him, and he couldn't bring himself to face his friends.

Knock, knock, knock.

Well, now he didn't have a choice. They were probably wondering why he had turned up and not come out of the Tardis. So with a deep, yet shaky, breath, the Doctor composed himself and walked towards the door, opening it.

This was not Victoria London. This was 1991 London. And standing right outside his door was a little girl, must have been no older than 10 or 11, who looked so much like her. Same blonde hair, although a shade darker. Same nose, same mouth. But her eyes, her eyes were wrong. They weren't a dark brown, they were a bright blue. Blue like the Tardis.

"Hi dad."

The Doctor stared at the little girl blankly. Dad? Did he hear her right? Did she just call him dad? He hadn't been a father since... well, since Jenny. His Jenny. She only lived for barely a day, and Cobb had shot her. Well, he aimed at the Doctor, but Jenny shielded her father. Taken the bullet for him. And she barely had begun to live.

And now a little girl stood in front of him, calling him dad. A girl who looked so much like his Rose, it was painful. His pink and yellow human. The Doctor fell to his knees, leaning against the side of his Tardis. He was in shock.

A small hand brushed against his cheek, and he noticed that the little girl was wiping away his tears. He was crying. His green eyes gazed up at her big blue ones.

"Why are you crying?" she asked innocently. She wrapped her small, thin arms around his neck and sat down in his lap. The Doctor hesitated, then wrapped his own long arms around the tiny frame, burying his face into her hair and crying.

She had to be hers. She was a spitting image. But how did she get here? And where was Rose? No, he'll worry about that later. Right now he was holding onto something that connected him with his Rose.

"It's okay, Daddy," the little girl whispered, patting his head. "Mommy brought me here. She said to wait for you. Wait five and a half hours. So I did."

That sentence shot a stabbing pain through his hearts. Wait five and a half hours, that's what he told Rose a long time ago. And now here was this little girl repeating those words he said all those years ago. He pulled away to look at the little girl in the face.

"Where is she now?" The Doctor asked, tears blurring his vision. The girl cocked her head.

"Went looking for Uncle Jack," she told him. "Said 'don't know how long it will take' and to give you lots of love." A pang of jealousy went through him, but he shoved it aside. Rose went to look for Jack because he was like a brother to her. And Rose wanted the Tardis family together.

"So you are Saphira's father?"

The Doctor looked up to see a stern looking, older woman in emerald green robes standing not too far away. Although her posture was that of a stern person, her face was soft from watching the reunion of father and daughter. My daughter.

"I suppose I am," the Doctor said shakily. "I'm the Doctor."

"Then you are her father," the older woman informed the Time Lord. "I am Professor Minerva McGonagall. Yes, I know that it's all in the books- Miss Tyler informed me- however the books no longer exist; it is all reality. And your daughter is a witch."

"I get to learn magic!" his daughter, Saphira, exclaimed. Saphira, like the dragon from Eragon. Rose must have named her that because of her blue eyes. He hoped her to be as wise and beautiful as her dragon namesake.

"And we wish that you would teach Muggle Studies for a few years, so that you would be able to keep an eye on your daughter and teach her things she wouldn't learn from us," Minerva explained.

Him? Teach Muggle Studies? He did a teaching job once, and he ended up having to blow the school up to get rid of aliens. And now here was a witch whom he had read about in the Harry Potter books, asking him to teach. Teach magical children about the ordinary world. But was the world ordinary? One part of it was all magic and the other science. Well... there was always the possibility that he could help integrate the two worlds together. And he had Saphira, Rose, Jack, and possibly Minerva and Dumbledore helping. Saphira could help by converting the children (okay that did not sound right. Much to Cyberman-ish). Rose would be his assistant teacher. Jack? Well he could work on the 'muggle' side of things.

"Please daddy?" Saphira begged, her big blue eyes staring imploringly up at him. Great Rassilon, Rose taught her the puppy look. The look that always seemed to win him over, even though he was over 9 centuries old (just how old was he now?)

"Okay then," the Doctor agreed. "Call me Professor John Smith."

"Actually, we have told everyone that you are Professor Evans," Minerva corrected, peering down at the Time Lord. That was when the Doctor realized he was still sitting on the ground with Saphira in his lap. "I think you've used John Smith a bit too much that's become a bit obvious, don't you agree?"

"So our family name is Evans? Saphira Evans, sounds like a beautiful name," the Doctor said, standing up. Saphira hopped off his lap, preening under the praise. "Rose Evans. Also beautiful. What shall my first name be, then?"

"You have a while to think of one. Tomorrow, I will take you both to Diagon Alley," Minerva said, leaving. "And Doctor," she called, "do take care of that family of yours. They are truly quite loyal to you." With that, the older woman left.

"So, do you want to go somewhere before we go Diagon Alley?" the Doctor asked, looking down at his daughter. He wanted to spend time getting to know the little girl before she was too occupied with school and friends. "Anywhere you'd like."

"Ooo, can we go to Disney World? Mum and I went there when the Vortex Manipulator accidentally overshot our destination and landed in Florida, summer, year 2006," Saphira replied. She was already starting to sound like a proper little Time Traveler already. "Oh, and can we take Harry with us? Mum gave me a background of Harry's past, and can we adopt him? I want a brother, and Harry would make an awesome brother. Oh, and I can't wait to meet Jack, he's going to pretend to be Mum's half-brother, so that's why I call him Uncle Jack, so that I don't make any slip-ups. Speaking of slip-ups, Mum told me about the time you both met Queen Victoria and saved her from a werewolf, and that she knighted both of you and banished you after wards! Ooo, do you think I'd get to meet a werewolf? Werewolves are awesome! So are dragons! I want to see a real dragon!"

"Blimey, you've got quite the gob," The Doctor interrupted when she paused to catch a breath.

"Yeah, Mum said that I get that from you," Saphira said, grinning cheekily. "So, can we take Harry with us to Disney? Oh, let's go in 2007, so that we don't run into Mum and I from the past."

"And how are we going to get Harry to come with us?" the Doctor asked. He wanted see how clever his daughter already was.

"We could kidnap him," she suggested. "Park the Tardis somewhere Harry runs when he's being chased by Mudley- I mean Dudley- and his friends, and he would run straight into it. Or so that it looks like a good hiding place. Park the Tardis on a corner, keep the door unlocked, and he'll use it as a hiding place. Or we could materialize the Tardis around him when he's with his relatives and give them a shock."

"Both of the first ideas sound good," the Doctor mused, "last one sounds brilliant, but we're not doing that."

"Nuts," Saphira huffed. "But we are taking Harry along, right?"

"'Course we are," the Doctor replied, walking back into the Tardis. His daughter followed him, and gave an excited squeal.

"Oh, she's absolutely beautiful!" she said, turning to take in her surroundings. The Doctor smiled, and the Tardis gave a pleased hum that sounded oddly smug. He would have to ask Her about that later.

Amy and Rory were gone, but the Doctor would keep going, for them. His Rose was coming back, and so was Jack. It would be the old team again, before the Game Station happened. But this time, they would have a few additions to the team. He grinned down at his daughter, and she mirrored the smile as he set the Tardis in motion.

Maybe he should be thankful that the Tardis took him to his daughter, instead of Victorian London. Who knew how long he would last before he was traveling again?

A/N: Don't worry, I'll be bringing Clara in at one point. She has started to grow on me. Hope you like the first chapter on my Doctor Who/Harry Potter crossover.