Some people think Amy has been taken since halfway through season 5, since “River is the only water in the forest - the forest on the spaceship - AmyPond was in fact, already a flesh copy as seen in The Rebel Flesh/The Almost People.
Look at this:
And then.. look at this comment:
I just realized that the title of the second episode of the Byzantium storyline (S05E05) was “Flesh and Stone”
Flesh and Stone
FLESH AND STONE
Okay. Okay then. That’s fucking awesome? That’s fucking awesome. But if it’s true…then you better have a REALLY FUCKING GOOD REASON FOR IT. Because that’s like…that’s a long time.
Discussed this with a friend, thought to discredited it if only because the season finale of series 5 was so major and already timey wimey twisted…
Notice River is wearing the same outfit she wore in eps. 1+2 in the promo pic but is wearing that pimped out dress in the episode preview? I bit this is where the scene with naked!River from the original season 6 trailer fits in! Is she gonna strip out of that dress into her ‘battle wear’ in front of the Doctor? If she is I can’t wait to see his reaction. I predict epic flailing and flustered panic :D!
And if the astronaut in Ep 1 was the little girl, like she was at the end of the episode and so on, then what we speculated all along was true: River kills the Doctor.
This actually fits with the “next time” trailer where someone is saying a baby is not a weapon. Was Melody engineered to have Time Lord-like abilities to be used as a weapon against River?
Maybe River didn’t know it was the Doctor she had to kill. Maybe she only knew that she had to kill someone at the time. Once she figured it out, maybe this entire time she’s been trying to stop it?
Maybe THAT is why she and the Doctor keep meeting out of order, because she’s deliberately trying to avoid it?
River Song kills the Doctor. We’ve kind of had a hunch since Time of Angels. But the revelation, the way it’s been revealed — THAT is going to be the cliffhanger. Because we’re seeing things in reverse and getting bits of information that don’t quite fit together until the finale when we find out who that little girl is.
So basically (may differ slightly to above theories):
Amy is giving birth to whatever The Silence impregnated her with. (They replaced her with a conscious ganger to travel with The Doctor while entrapping her in a maternity ward with the midwife)
This happened in Day Of The Moon and when The Silence said “You will bring The Silence” the silence actually meant The Doctor’s death
They want to kill The Doctor for his TARDIS/body
The TARDIS has regenerative powers, as does a Timelord’s body.
Using these regenerative powers of either TARDIS/Timelord and harnessing them, The Silence can awaken an army of Dead Silents that The Doctor ultimately killed with the sub-conscious message in the moon landing.
So they use the DNA of a Timelord which they acquire from ‘House’ (The Doctor’s Wife) who has been killing Timelords and collecting TARDISes to plant into Amy.
They do this by creating cracks to outside of the universe, which is where ‘House’ is, meaning they have been on this mission throughout series 5.
Now ridden with Timelord DNA Amy gives birth to the little Timelord girl who The Silence can then use in their controllable suit.
The girl is the only one powerful enough to kill The Doctor with a beam of energy (regenerative energy)
Now The Doctor is dead they can acquire (or try to) his body / TARDIS for the rebirth of their species and the ultimate invasion.
Im not sure as to why The Doctor was so submissive to his death, so that would have to fit in somewhere.
Interestingly enough this is similar to how Jenny was created (DNA of a timelord) and therefore proves this theory is possible OR Jenny is part of the equation)
Also now Amy has a Timelord all of The Doctor’s enemies are out to get it / trying to prevent The Silent’s plans (The ‘vampires’ seemed afraid of The Silence in Vampires In Venice)
Add any theories you may have to this post and the fandom together may find a correlation or link.
RIVER: I just landed her. THE DOCTOR: But, it didn’t make the noise. RIVER: What noise? THE DOCTOR: You know the— [impersonates TARDIS] RIVER: It’s not supposed to make that noise. YOU leave the brakes on. THE DOCTOR: Yeah, well, it’s a brilliant noise. I love that noise.