Amy still a poisoner in the nursery but now she alone, her daughter is taking away from her, praying that the Doctor and Rory are coming, but then she got a visitor, one of the soldier her name is Lorna Bucket.
Lorna: Sorry. I shouldn't be here. I'm meant to be at the thing. I brought you something. Your child's name in the language of my people. It's a prayer leaf and we believe, if you keep this with you, your child will always come home to you.
Amy: Can I borrow your gun?
Lorna: Why?
Amy: Because I've got a feeling you're going to keep talking. (facing back to the window as Manton continue talking to the soldiers about the Doctor) They're talking like he's famous. The Doctor isn't famous.
Lorna: He meets a lot of people. Some of them remember. He's sort of like a, I don't know, a dark legend.
Amy: Dark? Have you met him?
Lorna: Yeah. But I was just a little girl.
Amy: So was I.
Lorna: You've been with him a long time, then.
Amy: No. He came back for me.
Lorna: You must be very special.
Amy: Hey. You can wait a long time for the Doctor, but he's worth it, okay? The thing is, he's coming. No question about it. Just you make sure you're on the right side when he gets here. Not for my sake, for yours. (Holds out her hand and Lorna gives her the prayer leaf) Thank you.
As Lorna leaves to head back to her post, Amy holds the prayer really tight, still praying that her boys are on their way, and oh yeah she was right, The Doctor has arrive.
The Doctor: Amelia Pond! Get your coat!
But he didn't came alone, he brought an army, Silurian, Judoon, Commander Strax, Madame Vastra and Jenny, Dorium, Captain Avery and his son and of course Rory, as they launch a surprise attack and secure the base. But then Amy heard a knocking at the door as she trying to find something to use as a weapon.
Amy: Who's that? Who's there? You watch it, because I'm armed and really dangerous, and cross.
Rory: Yeah, like I don't know that.
Amy: Rory? Rory, is that you.
Rory: Yeah, it's me. Look, hang on a minute.
Rory is using the sonic to open the door
Amy: They took her. Rory, they took our baby away.
Rory: Now, Mrs Williams, that is never, ever going to happen.
Amy was shock to see Rory carrying Melody, he got their daughter back, she save.
Amy: Oh, my God. Oh, my God. Where's she been? What have they done to her?
Rory: She's fine. Amy, she's fine. I checked. She's beautiful. (Starts crying) Oh God, I was going to be cool. I wanted to be cool. Look at me.
Amy: You're okay. Crying Roman with a baby. Definitely cool. Come here, you.
They kissed in tears, they are reunited together and reunited with their daughter.
The Doctor: Urgh. Kissing and crying. I'll, I'll be back in a bit.
Rory: Oi, you. Get in here, now. (The Doctor heads down to see Melody for the first time) My daughter. What do you think?
The Doctor: Hello. Hello, baby.
Amy: Melody.
The Doctor: Melody? Hello, Melody Pond.
Rory: Melody Williams.
Amy: Is a geography teacher. Melody Pond is a superhero.
The Doctor: (sniffs Melody) Well yes, I suppose she does smell nice. Never really sniffed her. Maybe I should give it a go. Amelia Pond, come here.
Amy: Doctor.
The Doctor: I'm sorry we were so long. (Hugs and sniffs Amy)
Amy: It's okay. I knew you were coming. Both of you. My boys.
The Doctor: It's okay. She's still all yours. And really, you should call her mummy, not big milk thing.
Amy: Okay, what are you doing?
The Doctor: I speak Baby.
Amy: No, you don't.
The Doctor: I speak everything, don't I, Melody Pond? (Melody gurgles and the Doctor straightens his bow tie) No, it's not. It's cool.
The Doctor heads into the TARDIS to get something, Amy went with him but she came out as Melody started to cry.
Rory: Hey, what's wrong?
Amy: She doesn't like the Tardis noise. I asked him to turn something off, but it was all, but I don't want to punch a hole in the space-time continuum.
Then the Doctor came out of the TARDIS carrying an old fashioned cradle.
Amy: What's this?
The Doctor: Very pretty, according to your daughter.
Rory: It's a, it's a cot.
The Doctor: No flies on the Roman.
Vastra (oc): Doctor, we need you in the main control room.
The Doctor: Be right there! Things to do. I've still got to work out what this base is for. We can't leave till we know.
Amy: But this is where I was? The whole time I thought I was on the TARDIS, I was really here?
The Doctor: Er, Centurian, permission to hug?
Rory: Be aware, I do have a sword.
The Doctor: (Hugging Amy) At all times. You were on the TARDIS, too. Your heart, your mind, your soul. But physically, yes, you were still in this place.
Amy: And when I saw that face looking through the hatch, that woman looking at me.
The Doctor: Reality bleeding through. They must have taken you quite a while back. Just before America.
Rory: That's probably enough hugging now. So her Flesh avatar was with us all that time. But that means they were projecting a control signal right into the TARDIS wherever we were in time and space.
The Doctor: Yeah, they're very clever.
Amy: Who are?
Rory: Whoever wants our baby.
Amy: But why do they want her?
The Doctor: Exactly.
Rory: Is there anything you're not telling us? You knew Amy wasn't real. You never said.
The Doctor: Well, I couldn't be sure they weren't listening.
So as the Doctor heads to the control room, Amy and Rory get to spend time with daughter until Drax arrive with Lorna, she try to warn them that it's a trap by Madame Kovarian, and then the lights goes out.
Lorna: It's starting. Please, listen to me.
Meanwhile in the control room the Doctor, Vastra and Dorium are talking about Melody.
Vastra: Now, I have a question. A simple one. Is Melody human?
The Doctor: Sorry, what? Of course she is. Completely human. What are you talking about?
Dorium: They've been scanning her since she was born, and I think they found what they were looking for.
The Doctor: Human DNA.
Vastra: Look closer. Human plus. Specifically, human plus Time Lord.
The Doctor: But she's human. She's Amy and Rory's daughter.
Vastra: You've told me about your people. They became what they did through prolonged exposure to the time vortex. The Untempered Schism.
The Doctor: Over billions of years. It didn't just happen.
Vastra: So how close is she? Could she even regenerate?
The Doctor: No, no. I don't think so.
Vastra: You don't sound so sure.
The Doctor: Because I don't understand how this happened.
Vastra: Which leads me to ask when did it happen?
The Doctor: When?
Vastra: When did this baby begin?
The Doctor: Oh, you mean, Well, how would I know? That's all human-y, private stuff. It just sort of goes on. They don't put up a balloon, or anything.
Vastra: But could the child have begun on the TARDIS in flight, in the vortex.
The Doctor: No! No! Impossible! It's all running about, sexy fish vampires and blowing up stuff. And Rory wasn't even there at the beginning. Then he was dead, then he didn't exist, then he was plastic. Then I had to reboot the whole universe. Long story. So, technically the first time they were on the TARDIS together in this version of reality, was on their…
Vastra: On their what?
The Doctor: (gulps) On their wedding night.
Lorna was right it was a trap by Madame Kovarian, the TARDIS is blocked by a forcefield. They are attacked by the Headless Monks, and several Silurians are killed immediately. Dorium is beheaded, Meanwhile, Kovarian, well away from the base, contacts the Doctor, explaining they will be using Melody as a weapon in the war against him.
The Doctor: A child is not a weapon!
Madame Kovarian (on screen): Oh, give us time. She can be. She will be.
The Doctor: Except you've already lost her, and I swear I will never let you anywhere near her again.
Madame Kovarian (on screen): Oh, Doctor. Fooling you once was a joy, but fooling you twice the same way? It's a privilege.
The Doctor: Amy… Amy!
The Doctor just realize that Madame Kovarian has the real Melody the hall time and Amy has the flesh vision of Melody, The Doctor races to the hangar to warn his friends, but it was too late, Madame Kovarian open a slide panel and she saw Amy holding Melody as the battle continues, Melody saw Madame Kovarian face.
Madame Kovarian: Wakey, wakey, kid.
Amy heard her voice.
Amy: "What" oh no you don't, stay away from my…
But it was too late, Melody melted into flesh, Amy shock and in horrified that her daughter is gone.
Amy: Rory! (Screams) RORY! RORY!
Rory heard Amy scream, The Doctor arrive too late the battle was won, but the child was lost.
Amy: (in tears) So they took her anyway. All this was for nothing.
The Doctor: I am so sorry.
Then River Song arrive and the Doctor berates her for not helping. She tries to explain she could not have interfered in these events, and tells the Doctor what transpired was partially his fault, having been brought about by those who feared his reputation. The Doctor becomes angry and demands to know who she is. River shows the Doctor the cot, and the Doctor recognises River's identity.
The Doctor: Vastra and Jenny, till the next time. Rory and Amy, I know where to find your daughter, and on my life, she will be safe. River, get them all home.
Rory: Doctor!
Amy: No! Where are you going? No!
The Doctor takes down the forcefield around the TARDIS and goes inside. The TARDIS dematerialises. Then Amy talks to River
Amy: Where's he going and what did you tell him?
River: Amy, you have stay calm.
Amy picks up a gun, and aims it to River
Amy: Tell me what you told the Doctor.
Rory: Amy, no. Stop it!
River: It's okay, Rory. She's fine. She's good. It's the TARDIS translation matrix. It takes a while to kick in with the written word. You have to concentrate.
Amy: (looks at the Gallifreyanon the cot) I still can't read it. (Rory takes the gun away from Amy)
River: It's because it's Gallifreyan and doesn't translate. But this will. (gives Amy the prayer leaf) It's your daughter's name in the language of the Forest.
Amy: I know my daughter's name.
River: Except they don't have a word for Pond, because the only water in the forest is the River. The Doctor will find your daughter, and he will care for her whatever it takes. And I know that.
As Amy and Rory stare at the prayer leaf, the writing is translated into English, revealing the child's name: River Song.
River: It's me. I'm Melody. I'm your daughter.