Author's Note: The passages in bold are religious texts of the Silence. The one that is both bolded and italicized is taken directly from the television show.

Chapter 15: The Silence

"This was exactly you all this all of it. You make them so afraid. When you began, all those years ago, sailing off to see the universe, did you ever think you'd become this? The man who can turn an army around at the mention of his name, Doctor, the word for healer and wise man, throughout the universe. We get that word from you, you know. But if you carry on the way you are, what might that word come to mean? To the people of the Gamma Forests, the word 'Doctor' means mighty warrior. How far you've come. And now they've taken a child the child of your best friends and they're going to turn her into a weapon, just to bring you down. And all this, my love in fear of you." – River

"Annihilate? No. No violence, do you understand me? Not while I'm around. Not today, not ever. I'm the Doctor, the Oncoming Storm." – The Doctor

Amy pasted on a smile and tried to put a spring in her step as she walked into the sickbay. She'd made a quick detour to the kitchen on her way and picked up some food for the three of them. She was determined to be strong for them.

"Food first then questions." She announced before River could start what was sure to be a relentless flood of questioning.

River stared at the ceiling for a few minutes after she finished eating. "I don't even know where to start," she admitted.

"I could tell you what I've learned about the Silence," Amy offered.

"That works," said River.

Amy settled herself more comfortably in her chair and started speaking.

"You know the Silence is a religious order." River and Lucy nodded. "They are a secretive religion, but I was able to get my hands on some of their religious texts. I've only had time to go through a fraction of them, and what I've found so far is badly fragmented. I'll share what I have so far and would welcome any help in going through the rest of the texts."

She pulled a large, ancient looking book from her pocket. River looked at the book and back at Amy's pocket. Amy had managed to get the Doctor's pocket expanding trick to work for her because there was no way a book that large would normally fit into a pocket that small. Amy flipped through the book until she found the passage she wanted.

"The following is taken from the oldest text I was able to find:

'Before there was a beginning there was a Storm, and in the Heart of the Storm was all that ever had been, all that there ever would be, all that was, and all that could be.

Out of that storm the Universe was birthed. The lightning sparked stars, the thunder created planets, the rain gave brought forth all life, and the wind bound every part to each other. The Chosen worshiped and it was good.

Discord crept into the Storm, and it was both new and had always existed. The Storm became flesh, and the Heart walked among the stars. The Chosen wept.' – Book of Beginnings Chapter 1 Verses 1-3

I think the Silence believe the Doctor is the Heart of the Storm. They treat him as both their Devil and their God. He's been called the oncoming storm, the lonely god, and he himself said it was possible for him to be a vengeful god. Colonel Manton made it a point to tell his soldiers the Doctor was neither a devil nor a god. Why would he do that unless his soldiers believed he was one or both of those things? His childhood nickname was Theta Sigma which in early earth history often was used as an abbreviation for god. You even left him a message including those symbols when you were telling us to join you for the opening of the Pandorica."

River's eyes widen. "I don't remember doing that."

"Have you looked through the information I gave you on your replicas yet?"

"I only looked at the information on the replica who died in the library. I needed a break after that."

Amy nodded her understanding. "When you feel up to it look up anything they have on the Pandorica. Maybe it will help you think of something.

A few hours passed as River and Amy continued to discuss the verses. Lucy didn't say anything, but she occasionally nodded in agreement to comments the other two made. Amy finally broke off the discussion to make sure everyone ate again and then declared it bedtime.

The next morning Amy dragged a large stack of books, scrolls, and ancient bits of paper into the sickbay and they started again. Over the next few weeks the three women settle into a routine. They relaxed a little, and jokes were once again heard in the TARDIS. River and Lucy moved out of the sickbay and into rooms of their own. Lucy found the swimming pool by falling in one morning as she was looking for the kitchen. They spend most of their days helping Amy go through the mounds of texts she'd acquired about the Silence. River was starting to wonder if Amy slept. No matter how early she got up Amy was already in the library a glass of tea or cocoa in one hand and papers in the other.

One morning River was midway through a scroll that was mainly a mess of blots and water damage when she looked up and yelled, "I recognize something!" She points at a few words that are barely visible under a constellation of blotches. "It says, 'Demons run,' and further down here it says 'love lies' and at the very top," River runs her finger up the scroll. "Yes! It says the 'Book of Prophecy Chapter 11.' I know this. I was taught it as a child." River closes her eyes and recites:

'Demons run when a good man goes to war.

Night will fall and drown the sun

When a good man goes to war.

Friendship dies and true love lies,

Night will fall and the dark will rise

When a good man goes to war.

Demons run, but count the cost.

The battle's won, but the child is lost.' – The Book of Prophecy Chapter 11 Verses 3-6

Amy gets up and starts pacing. "It's obvious you are the lost child. I suppose Rory could have been the good man, but based on what we know so far I'm willing to bet it's the Doctor."

River scrunches up her forehead. "I agree, but what about the demons? It doesn't make much sense that the Silence would call themselves or their allies demons."

"The Doctor!"

"What?"

"The Doctor is both the good man and the demons. He is both the sun and the night. He is running from himself."

Lucy interjected, "What about 'friendship dies and true love lies?'"

"True love lies." Amy muttered increasing the speed of her pacing. "The obvious interpretation is that someone's true love lied which if the whole thing focuses on the Doctor it would suggest you lied, River."

River looks affronted. "I thought everything I said that day was true."

"Not exactly helpful." She stops pacing and runs out of the room. A few minutes later she returns with a pile of papers.

"Here you go," she says as she hands River and Lucy piles of papers. "This is transcript of everything River said in regards to the events of Demons Run starting with Rory's visit."

"How in the universe did you get that?"

Amy looked momentarily embarrassed. "Can't tell you right now."

Amy resumes pacing while the other two read the transcripts. "What do we know? Focusing only on your claims in regards to Demons Run we get:

1. You couldn't be at Demons Run until the end

2. It was the day the Doctor learned who you are

3. You couldn't have prevented the events of Demons Run

4. The events were the fault of the Doctor

5. You were Melody my daughter

"We know the last one is a lie. What about the rest? What if it isn't anything you said but instead some part of the verse is the lie or lies? What if true love is a lie? The lie could be your love of the Doctor, or it could be Rory's and my relationship that is the lie since he only existed through me. My friendship with the Doctor didn't die. Could they mean Rory's friendship with the Doctor?" Amy stopped pacing and collapsed into a chair. "Maybe I'm thinking about this too literally. We need more information."

Amy spoke incredibly quickly and once again River was forcibly reminded of the Doctor. They stayed up talking far past what River and Lucy normally considered bedtime only stopping when Lucy fell asleep sitting up.

River and Lucy had been on the Tardis nearly a month when River couldn't find Amy one day. She checked every room she could find, and finally decided that Amy would find them when she was ready. It took Amy two days to emerge. She just popped up in the library one morning. River took one look at her drawn face and decided not even to ask where she'd been. Lucy went to the kitchen and returned with tea and biscuits she made sure Amy consumed. It wasn't until the next morning that Amy even talked to them beyond an occasional "yes" or "no" answer.

"Amy, you need to start trusting me, it's never been more important." – The Doctor

"But you don't always tell me the truth." – Amy

"If I always told you the truth, I wouldn't need you to trust me." – The Doctor

Amy Pond was furious, and she was screaming at a dead man. She'd long ago moved her belongings into the Doctor's room. She'd felt a little guilty, but she couldn't go back to the room she shared with Rory. That part of her life was done, and any other room was far too lonely. The Doctor's things were nearly all as he left them. Amy had only straightened up a little and shoved his clothing into the back of the closet to make room for hers. The room smelled like him still, and it was an enormous comfort to lie back in the big bed, close her eyes, and imagine he was still alive.

With River and Lucy on board she was less lonely than she had been since the day Rory died, but River brought back so many painful memories. When she just couldn't stand his absence any longer she rooted in the back of the closet until she found one of his jackets. That night she fell asleep clutching it. A few hours later she woke up to something digging unpleasantly into her side. She had rolled over onto the Doctor's jacket during the night and something from one of his pockets was poking her. The TARDIS turned on the lights for her and bleary eyed she dug into his pocket until she pulled out a blue book, a TARDIS blue book, his diary. She didn't even hesitate before opening it and beginning to read. An hour later she was in the TARDIS's secret room screaming at a dead man.

"You knew! How long? HOW long Doctor!" And then she's not even sure what she's saying. She just knows that he can't hear her can't see her, and the mixture of sobs and words she's throwing at him can only rebound on herself. Eventually she runs out of words and out of tears. She wakes up hours later stiff from sleeping on the floor and moves to the small couch in the corner.

She starts talking to him again. "I found the prophecy. Found it in your diary. It'd be easier if I could hate you. I can't. I'm angry far angrier than I've ever been, and I'm hurting, but I can't hate you. You always thought you knew best. You lied to protect us, but that wasn't your responsibility. You failed to trust me. You wanted my unconditional trust, and I gave it to you. Did you ever trust me?"

Amy stayed in the secret room, the Doctor's tomb, for nearly an entire day before sneaking back to the bedroom that used to be his. It took her another day before she could face River and Lucy and one more after that before she could share what she'd learned.

"Memories are more powerful than you think, and Amy Pond is not an ordinary girl. Grew up with a time crack in her wall. The universe pouring through her dreams every night." – The Doctor

"Oh, Mummy, Mummy, pay attention. I was trained and conditioned for one purpose. I was born to kill the Doctor." – River

"Demons Run, remember? This is what they were building, my bespoke psychopath." – The Doctor

The third day after Amy found the bit of paper folded up in the Doctor's diary she managed to bring it up with River and Lucy. When they wandered into the library that morning she studied their faces memorizing their expressions. She was afraid of how their faces would change after she told them. She finally took a deep breath and announced, "I found something."

She pulled the ancient bit of paper out of one of her endless pockets and carefully laid it on the table in front of her. She made eye contact with River and then Lucy. This one is important. The translation is a bit," she waved a hand, "wonky. Whoever copied it from the original it seemed to have an obsession with rhyming. The results are mixed.

'Two women tied by time.

One for birth one for death.

One born free to a cage be bound.

Lost to silence she gives birth to sound.

Born from her body, yet not of her blood.

Created in darkness wanting to be found.

Belonging half to the flesh half to the sound.

Once of life twice of death

Time twisted a perfect breath

One to trust, one to lie,

True love to friendship die.' – Book of Prophecy Chapter 7, The Song of the Silence"

There is silence when she finishes reciting the prophecy. She hadn't needed the paper in front of her. The words were burned in her brain; she could see them when she closed her eyes. The other two women immediately pull the paper towards them to read it for themselves, and she starts pacing and talking.

"There's so much I'm guessing at and more that I don't know, but I believe you and I, River, are the two women bound by time. They have shaped our lives to fit what they think must happen. I am for birth you are for death. You were born from my body but not of my blood."

Lucy interrupted. "Technically she was born from my body. You only gave birth to a flesh replica."

Amy frowned. "It could be a translation problem, or perhaps it's not meant to be completely literal. The point is I think River and I are the tools they decided to use to remove the discord from the Heart of the Storm, and I think their plan revolves around the Pandorica.

Author's Note: Theta Sigma is shorthand for god found in Greek translations of the new testament. All of the names for the Doctor except the Heart of the Storm appear in Doctor Who canon.

Also worth noting is an older definition of the word bespoke is "engaged to be married."