So the deal is that when the drill hit the 21k mark or thereabouts, it activated certain "bioprogramming" in the dirt of the valley, which made it start eating people. Egregious: "Bioprogramming! Clever. You use biosignals to resonate the internal molecular structure of natural objects!" (Oh right, biosignals.) Anyway, Nasreen being a Woman of Science she is not having it, but the Doctor is still having Atreyu aftershocks, so he's flummoxed. But then even though the drill is stopped, there's still drilling happening, and the Doctor cutely lays down on the ground to confirm it: There's now somebody down there drilling up. Having been warned, no doubt, by the resonation of the "internal molecular structure" of "natural objects."
The Doctor, hacking into their computers, congratulates Nasreen and Mack on their jolly big fuckin' hole, and then asks them, um, why. They still don't have a compelling reason. Seems they found some blue grass and some anachronistic minerals on the surface, and thought, "Big giant hole." Then he uses their computers and a lot of talking talking talking to figure out that the things drilling up are numerous transports. The Doctor tells them to gather up Ambrose and Elliot, as the only people who live here in the valley, and get out of there because in twelve minutes the gnomes are coming.
Not gnomes. I wish. Mack totally goes, "How can something be coming up, when there's only the Earth's crust down there?" Good question. The answer is "I won't tell you, but I will continue to make extreme demands of you and get mad if you don't fulfill them unquestioningly, for no real reason." Maybe he's worried about Amy and that's why he's being such a dick? Except that he does this to Amy all the time, also.
Anyway, Rory comes running up and says the graves are eating people, and the Doctor tells him to get inside the church with the Macks, since there's now an energy bubble all around the whole area, which consists of absolutely nothing save: Two graveyards, a house somewhere, a Big Mining Thing, and a church. Very strategic, this town. The Doctor demonstrates the bubble by pulling a slingshot out of nowhere, and it's very cute. What is cuter than a bowtied boy with a slingshot? Only in shortpants could he compete with himself right now.