The train deposits them in the Great Pyramid. An American flag is painted on one side, along with "Area 52" in gigantic letters. So, they're not secret agents, then. Rory and Amy give the Doctor an eye patch to wear, which is really an "eye drive" memory storage device that allows its wearer to remember the Silence. Unfortunately it also renders its wearer unable to enjoy 3D movies. As they venture further into the pyramid, Rory shows him the fluid-filled tanks where they've imprisoned some one-hundred Silence. The tanks are to keep them from drawing electricity. So much exposition! Gah! Rory notices that the Silence are stirring a bit in the Doctor's presence and takes charge in a hot, efficient way. He sends some soldiers off to check something and the Doctor pulls him aside to have a private convo. "Always the loyal soldier, waiting to be noticed," he says. He tells Rory to ask Amy out. "She said that you were a Mister Hottie...ness!" See? Too adorably square for a Jack Harkness stag party. The Doctor goes on with his matchmaking, even though he knows it's an alternate reality that will soon no longer exist. He just likes to make me type things.
Finally, Amy and the Doctor make it into the base of operations. River's there, looking amazing, eye patch and all. Her hair is never, ever sad. A captive Madame Kovarian is also there, moaning about the end of time and all. "Oh, why couldn't you just die?" she asks the Doctor, disgusted. More exposition and we find out River used a bit of "hallucinogenic lipstick" on President Kennedy and Cleopatra to get the pyramids. Why wasn't that a whole episode in itself? It would be so much awesomeness. River and the Doctor banter a bit, much to Kovarian's boredom. The banter turns darker with River's professions of love and the Doctor's anger at her killing time. He advances on her. Soldiers grab him, but he breaks free and he latches onto River's arm. Time starts moving forward the instant they touch. Soldiers cuff his grabby little hands. "It's the only way, River, we're the opposite poles of the disruption," he says. "If we touch, we short out the differential! Time can begin again." But River's not having it, because it means going back to Silencio and killing him. Meanwhile, the Silence aliens are starting to break out of their tanks.
River and the Doctor are still arguing. "There are so many theories about you and I," she says. "Am I the woman who marries you or the woman who murders you?" Can't it be both? I mean, what a honeymoon! They seethe at each other a while before realizing that water is leaking from the ceiling. Kovarian says the Silence were never really trapped, but only waiting for the Doctor. Silence start zapping the soldiers. Rory joins Amy and the others, bolting the door behind him. The eye drives start crackling with bolts of electricity. A scientist falls dead. All the drives start shorting out. Amy and the Doctor pull theirs off. Much to Kovarian's surprise, her drive starts shorting out, too. Amy and River beg the Doctor to come with them to the top of the pyramid; they've been working on something to help him. Eventually, he goes with them, while Rory holds off the Silence, even as his eye drive starts shorting out. The Silence break through the barricade. "Rory Williams, the man who dies and dies again," they say. "Die one last time and know that she will never come back for you." But Amy does come back for him, and she brings a machine gun. She mows down the Silence and rescues Rory. Kovarian whimpers for help, her eye drive half off. Instead of helping, Amy reattaches the drive and sentences her to die. "River Song didn't get it all from you, Sweetie."