The school was a religious institution for children in need of psychiatric therapy. It was a beautiful cathedral with angelic statues guarding every gate and every corridor. Amelia would get visits from The Doctor and his associate Dr. Song for weekly check ups.
She spent 4 years as a student and patient at Father Octavian's school and a full recovery seemed within reach before things began to fall apart again. Quite literally; things fell apart after a clergy member was accidently killed by a statue of an angel falling from the 4th story balcony. Amelia's treatment and therapy stopped working soon after.
"Hello, Doctor" Amy smiled as Dr. Smith walked in.
"Hello, Amelia" The Doctor smiled back. "You're turning 13 next week aren't you?"
"That's right" Amy beamed.
"Do you think you might be ready to go back home for good?" The Doctor asked sitting at the armchair beside Amy's bed.
"I don't know if I want to go back. Not now that we have to stop the angels. I can't go back now" Amelia's eyes shifted back and forth. "Don't blink."
"The angels? Why do you think they need to be stopped?" The Doctor asked trying to hide the disappointment in his voice. He thought she was finally ready to leave the institute.
"They're killing people. I've never liked them. They make my eyes hurt." Amy rubbed her eyes and saw sand pouring out of them and onto her hands. "I'm turning to stone! Doctor, what do I do?!"
"Amy..." The Doctor took her hands in his. "I need you to trust me. Close your eyes and focus. Just listen to my voice." The Doctor kissed Amelia's forehead. He'd grown to care for her very much since they first met 6 years ago.
When Amy opened her eyes she found herself alone in her dormitory. The Doctor had disappeared and the angel behind her eyes was gone. She saw an empty bed beside hers and a crack in the wall of her dormitory.
"What happened to my roommate?" Amelia asked when The Doctor came to visit the following week for her 13th birthday.
"Which roommate?" The Doctor asked.
"Melody's not here. How do you explain the empty bed?" Amelia pointed to the bed behind her. "The crack in the wall erased her just like it erased the angels."
The Doctor didn't seem to know who Melody was but Amy did and Melody had always known who The Doctor was. Amelia had gotten older and understood that sometimes she imagined things but how could she have imagined something that felt so real. She had a roommate named Melody for years and now it was like she never existed.
Amy was eternally grateful to The Doctor for saving her from the angels and from her sickness. She found herself looking in the mirror to make sure she looked her best before The Doctor came in to visit. In the last 5 years she'd grown much taller and she looked less like a child and more like a young woman. She wanted to be a woman.
She wore her uniform skirt a little shorter and buttoned her blouse a little lower. She twirled her long red hair in her fingers when The Doctor spoke and imagined the two of them together. She'd toss and turn at night in her bed wishing for him to be beside her.
"I'm taking you back home, Amy." The Doctor sat beside her on her bed "You can be with Aunt Sharon again and you can see your old friends. You know Rory still asks about you?"
"He does?" Amy vaguely remembered a sweet little boy named Rory. She wasn't sure if he was real or not. She hated that she couldn't tell sometimes.
"Yeah, you remember him? I think he's a good friend. He might be good for you." The Doctor smiled.
"But what if that's not who I want?" Amy leaned in uncomfortably close to The Doctor.
"I'm not sure what you mean, Amy" The Doctor felt uneasy.
"Let me think of something simpler you can understand" Amy placed her hand on The Doctor's chest and leaned in for a kiss but The Doctor quickly dodged it and jumped off of her bed.
"No, Amy!" The Doctor found himself up against a blue wardrobe as Amy ran her hands up and down his chest and kissed him hard on the lips. "Amy, you're my patient you can't... you can't do this." He tried to speak between kisses. "I'm 32 years old and your 13, Amy!" He held her by the arms and pushed her back onto her bed. "We have to get you sorted out."
"That's what I'm trying to tell you" Amy leaned back on the bed smiling.
Dr. Smith quickly took her hand and got her to stand back up. "Listen to me. If you do this again I can't see you anymore. Do you understand? This isn't going to work."
Amy stood doe eyed and confused as she let it sink in. "I wasn't suggesting anything long term." She smiled seductively.
The Doctor quickly left her room and locked the door behind him. "She's 13, she's 13. She's Amelia Pond and she's 13." He whispered to himself over and over as he walked briskly down the corridor to Father Octavian's office to get his final approval to send Amy home.
Rory's mother advised him against it; but Rory wanted to be there when she returned. He'd thought about her everyday since they took her away. He wanted to know that she was ok.
Dr. Smith's associate, Dr. Song dropped Amelia off at Aunt Sharon's house. Sharon and Rory waved at her from the front door as she walked up to the house for the first time in nearly 5 years. Rory was surprised to see it was a tall beautiful redhead in a mini skirt who stepped out of the car. He was expecting a little 8 year old in a winter coat and mittens. Amy had grown strikingly attractive.
"Welcome home, Amelia" Aunt Sharon hugged her tight.
"Hi, Amy" Rory waved sheepishly.
Amelia smiled wide at the sight of her old childhood friend. He'd grown into a tall, lanky, goofy looking teenage boy with a dirty blonde mop for a head of hair and a nose too long for the rest of his face. But his sweet blue eyes were still the same. "Hello" Amy chuckled as she gave him a hug.
"You look amazing. I mean..." Rory stumbled over his words. "... that is to say.. umm you look good...you look well, I mean. I'm so glad you're well enough to come back home." Rory smiled and looked down at the ground when he spoke to her. He wasn't used to a beautiful girl actually listening to what he had to say.