She leads Rory to the temporal engine room where she's cobbled together a shelter. She's also cobbled together a pet hand-bot which she's named Rory and given a cartoon face. She's literally disarmed it; without its hands, it's harmless. She blasts the Doctor for "traveling through time on whimsy" while she's been stuck defending herself, alone. I know being alone for so long is bound to mess with one's mind, but come on. She knew from personal experience he had a penchant for showing up decades late and she signed on for the trip anyway. Plus, she and Rory really should have figured out which buttons to push. There are risks when you go time-traveling, so suck it up. The Doctor asks to speak with the Interface, so Amy and Rory go off to the garden because it doesn't work in the engine room.
She tells Rory she's reprogrammed the Interface. "It will tell me anything now except how to escape." Rory's impressed. The Doctor interrupts: "Temporal engines like that have a regulator valve that has to be kept a distance away from the reactor or there'll be feedback." He gets the Interface to show him where the regulator is and then asks Rory to give Amy the glasses. The Ponds joke that at least they look better than a fez. Amy's surprised to hear herself laugh. Rory wanders off so that Amy and the Doctor can go over some technical things together. He soon gets himself anesthetized by a hand-bot. He's only woozy for a moment before Amy comes along and beheads the hand-bot. The Doctor says he's figured out how to use the temporal engines to fold Amy's timestream in on itself. "Amy Pond, I'm going to save you!" he cries triumphantly. Much to everyone's surprise, she refuses.
She marches out of the garden with Rory trailing after her and heads back to the engine room. Rory sees a reddish smudge on the door and uses the time glass to show the message when it was fresh: "Doctor, I'm waiting." The Doctor looks devastated. Rory catches up to Amy. "Why won't you help yourself?" he asks. She points out that she -- the current version of herself -- will cease to exist once they rescue her past self. The person she is now will, in effect, die. So she asks them to take her as she is now. Rory has to choose which wife to save, but he's horrified at the thought of her being there even an hour, much less 36 years. Rory blames the Doctor. "This is your fault!" he rails. "You should look at a history book once in a while, see if there's a plague outbreak!" But that's not how he travels, the Doctor says. So Rory says he doesn't want to travel with him anymore, but I bet he will.