I don't know if Amy could hear Madame Kovarian when she said "Wakie wakie" to the Flesh Avatar of Melody, but for the sake of the story let's assume she could. Also, Puzzle Pieces in History, done from Rory's perspective, can be considered a companion to this; Rory focuses on some different aspects of the revelation, so I decided to cover other things from Amy's point of view. I own nothing.
There are horrifying things driving in her blood and infecting her mind. They scream and yawn and wake, and they bloom in her chest like a great, poisonous flower, taking away from her the right to breathe.
The sounds of gunfire echo all around and Amy holds Melody close to her chest, bouncing her and praying she won't start to cry out. If Melody starts to cry they'll hear her; if they're found she'll be taken away again. Amy doesn't think Rory would react too well if he was to find his infant daughter missing again and his wife dead with a hole in her chest—he'd probably hear the screaming and the swearing first though, and it would likely be the other man who was dead. Never underestimate the powers of an extremely cross mother.
"Wakie wakie." The whisper of a gravelly and horribly familiar female voice sounds behind Amy and her jaw clenches. You're just imagining it; she's not here, she can't be here, she left, ran away. She can never come near you or Melody again; you're just hearing things.
How much Amy wishes that were true later.
The weight in her arms vanishes, a puddle of pale goo splatters to the floor, and Amy is left clutching a blanket. Nonononono, please no, please no, please, please, please! Melody? Melody!
"R-Rory?" Amy can't find breath in her lungs and her blood is starting to burn. They've taken her. They've really taken her. She feels like the whole universe is crashing down and breaking her bones, one by one.
Then, breath returns and a terrible scream rips from her lungs.
"RORY!"
Nothing could have been more terrible than that, or so Amy thought at the time. Nothing more horrifying or more terrifying. There was nothing like that to take the ground out from under her feet, and there was nothing like the Doctor running away in the TARDIS to illustrate just how powerless she was in the long run. She could do nothing if he did not support her and that knowledge infuriated Amy more than anything could.
Nothing could be more terrible. Except, something is.
"I still can't read it," Amy declares, the gun clicking in her hand.
Rory grabs Amy's hand, the hand that has a gun directed straight at River Song's heart, and pulls it down, gently prying the gun away from her shaking fingers. Amy feels bile rise in her throat and it's all she can do not to scream at this woman: Where were you when my daughter was being stolen from me? Where were you when I needed you? Where were you when Melody needed you?
River is, if anything, completely unfazed; she even seems somewhat satisfied with Amy's reaction. This is all the proof Amy needs that this woman is completely mad, even more mad than the Doctor. No sane man or woman looks at someone holding a gun at them and says "It's okay Rory. She's fine; she's good."
But there's something else there, something beneath those inscrutable eyes, something like… Sadness, maybe? Pain? Whatever it is, Amy doesn't like it.
"That's because it's Gallifreyan; it doesn't translate." River reaches down into the cot and picks up the green prayer leaf the young soldier from before gave Amy. "But this will," she explains, her voice catching, as she takes Amy's hand and presses the prayer leaf into her open palm. "It's your daughter's name, in the language of the forest." A spasm of a smile shakes across River's lips.
"I know my daughter's name," Amy snaps.
"Except they don't have a word for 'pond'," River tells her gently, "because the only water in the forest is the river."
Amy feels her throat close again; river…
"The Doctor will find your daughter, and he will care for her whatever it takes." River tilts her head and stares hard at Amy, something foreign again creeping over her face. "And I know that." The finality in her voice is damning.
Amy stares down at the leaf in her hand, Rory peering over her shoulder. The glittering gold thread letters are starting to change. The first letter becomes an 'R'. Than an 'I'. 'V'. 'E'. 'R'.
This can't be real…
Fighting back the shake in her hands, Amy turns the leaf over, running her fingers across the satiny material.
'Song.'
Why?
Amy looks back up at River, and finds a face there as familiar to her as her own. "It's me." River's voice breaks on 'me'. An uncertain smile is there. "I'm Melody." She pauses and stares long at them both. "I'm your daughter."
Nothing is more terrible, Amy realizes, than the thought that her daughter will become River Song.
There was an air of mystery around River from the moment Amy first saw her over that video, winking roguishly up at the camera. She had this appeal, this glamour, a Devil-may-care attitude towards life. She could discard it in a second to become Doctor Song, professional woman, dealer in knowledge and ever practical and reasonable, but the wilder side was lurking just beneath the whole time, waiting. It just needed a chance.
Amy liked her at first sight. River was like this really cool big sister type. She could boss the Doctor around and one-up him every hour of the day, she let Amy in on little secrets—not important ones; just little ones—and winked at her whenever the Doctor started to splutter. The cool, knowledgeable big sister; that was how Amy saw her. She was absolutely outrageous, defacing a cliff face just to get the Doctor's attention, impersonating Cleopatra, carving words on a home box while wearing a black dress that looked like something straight out of a 40s noir film. If Amy had had a big sister she would have wanted her to be like River. So cool. So very, very cool.
Frightening things abounded around River, of course; a ton of frightening little things. There was that time when they were being chased by the stone Dalek in the museum and River told Amy and Rory to move on. When she rejoined them she said "It died" with a horrible sort of finality and Amy didn't have to wonder exactly what she'd done to it. And then, Rory told Amy about how River had shot and killed a Silent without even looking at it, all the while with this genial smile on her face. He'd said there was something mad about that smile.
Amy could believe him when she saw that cold, steely glint in River's eye just after Rory moved away.
River was dangerous; Amy knew that. No one who knew River could deny that she was anything but dangerous, a wild card, an unknown quantity, but she had enough humanity, enough grace, enough charm, enough compassion that Amy could look past that. All this time Amy had looked at River like this big sister she never had, and all this time River, she… Amy swallowed. River must have known the whole time. What that must have been like... Now she can understand the look on River's face at the reception for Amy and Rory's wedding when she passed by the window, and Amy feels sick.
In another time, another life, her daughter grew into this woman. Melody, her Melody, became a woman who could kill Daleks without batting an eye, could shoot a Silent down without looking at it, a smiling, glamorous, utterly merciless killing machine.
And the infant Melody who's been spirited away to parts unknown may well become River Song too.
My daughter's going to be a weapon, to bring the Doctor down. My daughter's going to be raised to kill him.
They must know what they're doing, this woman with the eye-patch and her people, if River Song is the result of it. These people, they know how to take an innocent little girl and turn her into a ruthless weapon if River Song is anything to go by.
Melody is River and River is Melody and this… This is entirely too real for Amy. She looks into this woman's eyes, tries to envision Melody becoming this and she can't. It's too real; it's too much, and Amy can't wrap her mind around it. She can't see Melody becoming River, can't see her daughter becoming a doctor with a gun, a convict with a past, a woman who killed a good man…
A woman who killed the Doctor.
River looks at her and smiles, uncertain and unbearably gentle, and Amy's mouth is dry and cracked. She doesn't know what to say to her, doesn't have a clue what to say.
She does know what she's going to do though, when she catches up with that woman with the eye patch. It's quite simple.
Amelia Jessica Pond is going to kill the woman who's taken her daughter. She's going to kill her for taking Melody Pond and turning her into River Song, going to kill her for taking a baby and turning her into a killing machine, for daring to think she can do this to her daughter. Amy doesn't know how she's going to kill her. Maybe it will be with a gun. Maybe she'll take Rory's sword and off her that way. Hell, maybe she'll get a laser beam and fry her brain. She might even kill Melody's kidnapper with her bare hands, wrap them around her throat and squeeze until that one eye rolls back in her head. She will kill her though.
It's a bit too late for River Song who stands before Amy now. It's not too late for Melody Pond. And this time, Amy will do whatever it takes, with or without the Doctor there to help. Nothing will keep her from her child. But something kept you from River in that other life—
No. This is different. I won't fail. I brought the Doctor back when reality kicked him out; I can do this.
River's still looking at her and Amy's heart is beating out of her chest, air never quite reaching her lungs. This is her daughter, and yet she isn't, and yet she is. Her daughter, the woman she up until now thought of as a big sister, a friend, in years so much older than Amy herself, looks at her and waits.
The daughter who isn't her daughter and yet is looks at her and waits and Amy can't think of anything to say. This is too real, too real and River's smile, God it looks just like Rory's. Come to think of it, Amy looks at River and realizes she looks just like Rory; How did I not see that before?
This is Amy's daughter, staring at her, all the layers of mystery finally stripped away, and leaving something unthinkable in its wake.
This is the most terrible thing.