Alright, here it is the last chapter in this story. Huge thanks too everyone who has read, reviewed and encouraged me through this story. I love you all.
Biggest thanks to lastincurableromantic for cleaning up this story and just being awesome.
Four days later, Rory and Amy sat on opposite sides of Melody's bed. Half an hour ago, Rory had unhooked all the monitoring instruments. There was no need for them anymore; it was only a matter of time before their daughter regenerated. Everyone had already said their goodbyes and the family had left Melody alone with her parents.
"I've made my choice," Amy said, brushing a strand of hair out of Melody's face. "After her regeneration, we'll take her to Hannah. Together."
She reached over and took Rory's hand. It was the first time she had purposely touched him since Jenny had brought Melody back to them. It felt good, it felt comforting and it felt like eventually everything would be alright. That maybe in the end their relationship would turn out to be stronger for it, eventually.
"We can't keep her here. If we did, she wouldn't exist… You wouldn't exist. The Universe needs you both." She squeezed his hand. "I need both of you, even if it takes me awhile to work through this. I know that you or Mum or Dad couldn't stop this and would have changed it if you could...it's just... I need time.
"Take as much time as you need," Rory said softly. "I love you, Amy."
"I love you and your stupid face, too." Amy gave him a small smile and looked back at Melody's face. "Mels and River have both said that they don't remember anything from before their first regeneration. It's probably for the best, yeah?"
"Yeah." Rory picked up his daughter's hand and kissed her knuckles. "I'll do it. After she regenerates and before we leave her with Hannah, I'll erase everything. Leave her with the knowledge of who she is and that we love her and that unfortunately this had to happen but it's not that we didn't want her."
Amy took a shaky breath. "She won't understand why until she's older. I wrote her a letter for Hannah to give her when she's a teenager. I think she'd like that." She paused for a minute before speaking again. "Are you going to leave something with her?"
"A book, one that will help her to know who she is as a Time Lord. All the things I wanted to teach her but can't."
"Mummy," Melody murmured, starting to wake up. "Mummy, it hurts."
"I know it does, baby. It's time to let go." Amy touched her face and thought about what the Doctor had told her to say. "You can feel that warmth, yeah? See the golden light in the back of your mind?"
Melody nodded and turned to her daddy. "What do I do?"
"Let go, love, just let go and all the pain will stop." Rory squeezed her hand. "You are a Time Lord, Melody Tyler-Pond, and it's regeneration."
They had talked to her about regeneration in the last few days. Had showed her pictures of all of her granddad's faces (once they had calmed her down and convinced her that she had in no way harmed him). Had convinced her that this was a good thing, and it was. It was infinitely better to have their little girl regenerate then to have her die.
"Will it hurt, Daddy?" Melody asked, her voice betraying the pain she felt as her internal organs shut down.
"No worse than it does now, sweetheart." He kissed her forehead. "And when it's over, the pain will be too. You just have to let go."
Melody's hand began to glow with an all too familiar golden glow. "It's started," she said, letting go of her dad's hand and holding it up in front of her face.
Amy kissed her cheek before stepping away. "We love you, Melody, so very much."
"I love you too, Mummy. Love you, Daddy." Melody breathed out the golden light. Rory helped her to her feet before moving to Amy's side. A few moments later, Melody exploded with regeneration energy. Amy buried her face in Rory's shoulder. He kept his eyes trained on his daughter's bubbling and contorting features. Her limbs shortened, her hair and skin darkened, every feature she had changed.
She was a younger version of Mels, a face he remembered from his childhood. A face he had known as a friend, not as his daughter.
When it was over, Melody lay sleeping soundly in the middle of the bed. Dad had warned them that regeneration in someone so young would be even harder on Melody than on someone even a few years older. Tenderly, Rory placed his fingers on Melody's temples. With great care he pushed into her mind and saw all the terrible things they had done to his daughter.
Yes, they had run experiments her, forced her to do things and they had broken her body. But they had also isolated her, kept her locked away from any human contact except for Kovarian or Dr. Renfro. They had taunted her with stories of her family and how they wouldn't find her until it was too late.
All of that hadn't broken her mind or her spirit. She had known they would come for her, take her away to a happier place. Their little girl was so strong, yet she was so burdened at such a young age. She didn't deserve that.
Carefully, Rory extracted her memories of her time of imprisonment. Not bothering to lock them away, just erasing them. Her memories post rescue, he locked away. He was careful to bury them deep enough that they would resurface on their own.
He also made sure to leave the knowledge of who she was. That she knew she was Melody Tyler, daughter of Rory Tyler and Amelia Pond. He left Tony, Mum and Dad in her memories as well. Sabrina, Jenny and Trisha were hidden from her and she would discover them on her own, in her own time.
When he was done, he gently pulled out of her mind, breathing heavily from the exertion. Melody would sleep for hours as her mind and body recuperated.
"Is that it?" Amy asked softly. "Her memories are gone?"
"Yeah." Rory nodded. "Can you hand me the earrings?" Amy handed over a box that had been sitting on a nearby table. The earrings worked like Rose's necklace had, as a perception filter. They were made from pieces of the Tyler family TARDIS, not the Doctor's, to bolster her connection to the ship she would be near when she was growing up.
They would help to shield her unique biology from prying eyes and help keep the family from figuring out her identity too soon. Rory affixed the jewelry to Melody's ears (luckily this regeneration had come with pierced ears) and he kissed her forehead.
"I'm coming with you," Amy said. "To take Melody to Hannah, I'm coming with you."
"Amy, you don't have to, if it's too hard…" he started.
"Of course it will be hard, but I am her mother. I have to be strong, for her." Amy stood tall, defiant. "I have to do this."
Rory nodded and scooped a blanket wrapped Melody into his arms. Amy grabbed the suitcase they had packed for her and followed Rory to the console room. The Doctor and Rose were waiting for them. His arms were around her in a hug and her face was buried in his neck. They were lost in their own world, their own grief, but turned immediately when they heard the other two enter the room.
"Are you sure you're ready," the Doctor asked, still keeping one arm around Rose. "If you need more time, we could…"
"No," Amy said, cutting him off. "It won't hurt any less to wait. As long as you have the files ready, then we should be off."
Solemnly, Rose and the Doctor piloted the TARDIS to the Brigadier's office at UNIT headquarters in 1993. When they landed, Rose went over to her granddaughter and placed a kiss on her cheek. "Be brave, we'll see you soon, love."
The Doctor led the way out the door holding the two blue folders containing all the information that Hannah would need to guide Melody. Amy gave a small wave to her mum and followed Rory, holding Melody, out the door. Taking their little girl onto the next stage of her life, one that was full of happiness and love, just not the way they wished it could be.
Six weeks later Amy sat on a bench in a park outside of London. No one knew she was here, except for Jenny who had left her alone to give her some privacy. Jenny had given her a sad smile the first time she'd agreed to chauffeur these trips. Amy needed some time apart from Rory and needed to make sure that her daughter was alright without them.
The year was 1994 and there was a group of children playing on the swings. Amy was being careful to stay far enough away to see the achingly familiar little girl laughing by the swings but to not look like a creepy stalker. It wasn't stalking if you were actually keeping an eye on your own daughter was it?
"Is this helping?" A familiar person asked as she sat down next to Amy.
"Somewhat," Amy answered vaguely, keeping her eyes focused one little girl as her foster mother called for her to leave. The pair on the bench were quiet until Mels Jones and her caretaker were out of sight. "Did you know I was here? The times I've come to watch?" Amy asked, turning slightly towards River.
"I knew." River closed her eyes and tapped her temple. "I could feel you, in here. Back then it hurt sometimes knowing that you couldn't say hello."
"I'm so sorry, Melody. If I could have changed it..." Amy's voice broke. "I could have changed it, but I didn't. I'm so sorry, love."
River reached over and took Amy's hand. "If you had changed things, if you had chosen the other path, you would have changed everything, not just who raised me. Nan and Pops would have never had Dad, nor would they have adopted Aunt Sabrina." She squeezed her mother's hand. "And what about you? You would have had a lonely childhood raised by a selfish woman who would have done anything to keep under her thumb."
"Sacrificing your happiness for my own, what kind of mother does that make me?"
"There would have been no happiness for me if it would have gone the other way, Mum. Do you understand that, I mean really understand that?" Rivers eyes were pleading for her to understand.
"Maybe it just hasn't sunk in yet. Still, I'm sorry, Melody."
"I know. But don't think I haven't had an amazing life overall." River smiled. "I have an amazing family, a good career. I've had some fantastic adventures, and I have Jack. And there is still so much left out there for me to see."
Amy couldn't help but giggle. "You and Jack, you're so cute together but Dad's face when he realized that Jack was involved with his granddaughter... Oh, that was priceless. It was one of the only things that have cheered me up these last few weeks."
"It was as big of a surprise to me as it was to you." River grinned. "It was complicated and it happened slowly, over almost two decades, actually. Sure, I knew him from when he visited everyone in Leadworth, but it was when he came to help me, after Berlin, that things changed. Now we've been together over a century."
"I can't imagine Jack Harkness being with only one person for that long." Amy giggled again.
"Who says he has?" She gave her mother a wicked grin and winked. "There's nothing wrong with being a little flexible in your marriage."
"River!" Amy swatted her daughter's arm. "That is not the kind of information that you share with your MOTHER!"
River shrugged. "You wanted to know if I was happy and I am."
Unable to control herself, Amy continued to giggle for a minute, and River joined in. To Amy it felt like it had been so long since she'd even had the urge to laugh.
"Where are you at, River, in your timeline?" Amy asked once she was able to control herself again.
"I'm going to do something I never do, Mum," River said in conspiratorial whisper. "I'm going to give you a spoiler."
"Oh yeah, and what's that?" Amy leaned in so the other woman could spill her secret.
"Promise you won't tell anyone?"
Rolling her eyes, Amy agreed, "I promise, now tell me already."
"The Library," River smirked. "I didn't die, for a moment I thought I would. But Dad... That was three years ago for me. So don't you worry about me, Mum. I'm always alright."
Amy stood up and dragged River to her feet. She then threw her arms around her daughter and hugged her so tightly, she feared that River's respiratory bypass might kick in. "Oh that is the best news I've heard in weeks. How? How are you saved?"
River managed to loosen her mother's grip. "Now that's a spoiler I can't tell you. But if you want to tell Aunt Sabrina to pass Dad the message Idris gave her, it couldn't hurt."
Unable to control herself, Amy began to laugh and jump around in celebration. A smiling River joined in. They were laughing, dancing and giggling; they didn't even notice when the slightly purple TARDIS materialized behind them. Jenny stepped out and observed the mother and daughter. "Am I interrupting something?" she asked, beaming at seeing Amy so happy.
Amy ran over and hugged her sister-in-law. "Everything is going to be alright, Jenny. It's all going to be alright, molto bene to quote Dad."
"It's so good to see you smile again." Jenny squeezed Amy tightly and then reached out a hand to River. "We need to go, but River, I know everyone would love it if you joined us for tea."
"At Uncle Tony's?" River asked, joining her mum and aunt in a group hug.
"Every Saturday night," Jenny replied with a nod.
River smiled and pulled away, taking hold of Jenny and Amy's hands. "Then I'm in. There's nothing more important in the Universe than family."