In this first part we see the mining crew, mining operations, etc. They reach a milestone of 21 kilometers deep, then go home for the weekend, leaving the night guy on watch. During the night an earthquake, he goes to investigate, and is sucked underground. When the Doctor, Amy and Rory arrive the next day we learn that some bodies have been stolen from their graves by being sucked underground. We also see Amy being sucked underground.
Interestingly Amy kinda gives up and allows herself to be sucked underground. Why? She's been shown to be a fighter but perhaps she's trusting the Doctor to save her.
The Doctor is shown giving promises to everyone that nobody dies. We've seen him in other episodes this season going to great lengths to save people, even at his own risk. This is a bit of a departure from prior Doctors, though not much as he has in many instances put himself at risk to save people. Including once actually going into regeneration to save the companion (the screeching b**tch, Peri, no accounting for taste).
The story starts with a straight-on shot of a small windmill, and the windmill appears in a later shot. Why? Are these common in the Welsh countryside? That's curious. It also starts with the young boy reading a monster story about creatures with fangs and claws, nice foreshadowing. Which makes it curious whether the windmill is foreshadowing or what.
Likewise they show a future Amy/Rory waving to them. Why? Of course the Doctor stops them from meeting themselves, don't want those time eater thingy's that look like they escaped from Harry Potter to show up again. But under that theory that every object shown on screen has to have a use later on, what's the purpose for showing a future Amy/Rory? And is it connected to the bit in Flesh and Stone where it appeared that a different Doctor showed up to comfort Amy immediately after the Doctor left to go to the control room? That is, are we seeing a convoluted timeline being shown through several episodes? Is there going to be a later episode where they have to go back to prior stories and affect the outcome of those episodes?
"That's breaking and entering"! Amy said that as the Doctor opened the lock letting them enter the mining compound. What's this hypocrisy coming from her? She, the one who exclaimed that she never let Keep Out signs stop her, being shocked about the Doctor waltzing past a Keep Out sign? It's Rory's job to be shocked at illegality.
"Silence, absolute silence" Okay, so the Doctor is asking for a moment to think. But it's a curious phrase to use considering the season-long threat about the Silence that is coming.
"I'll gladly die for my cause, what will you sacrifice for yours?" All season the Doctor has been shown repeatedly going to great lengths to save everyone. While not entirely out of character it's a bit further extreme than normal. In other words, the Doctor is not the sort of warrior that is willing to let companions die, or for himself to die, if it will further a given cause. Some warriors are willing to lay down their lives to further a cause. C.r.a.z.y.
This episode is setting up a conflict in the next. In all prior Silurian episodes the conflict was that the Silurians were intent on launching a war on Humans so the Silurians could regain their planet and rule their planet. The same is happening in this episode. The theory is that if the captive dies, the Silurians will use that as an excuse to actually launch the war, and cause a bunch of death etc. The Doctor is trying to avert the war. The captive appears to relish the idea that her death could launch the war. And in any case she's taunting the captors saying that one of them will kill her.
The question is: Who. Motive: Each has someone they love who has been taken underground by the Silurians. Means: A pile of guns and other weapons were shown. Three people guarding the captive, and apparently one of them will do the deed. Rory is shown with feelings of betrayal, as is the woman. The mining assistant might want revenge because of his impending death.