The Doctor wakes some time later on a train in a pretty nice office. In the background, a radio announcer is apologizing for the interference coming from recent solar flare activity. Amy's watching him from the doorway. "Those stun guns aren't fun," she apologizes. "I wanted to avoid a long conversation." She tells him to get up because they'll be in Cairo soon. The Doctor tries to talk her out of whatever evil plan she has, tries to make her remember him and their friendship in another reality, tells her she can see what others can't because of growing up with that rift in her bedroom. He realizes in mid-ramble that the walls are filled with her drawings of all their adventures. She has a little model TARDIS, too. She finally smiles at him and gives him a clean suit to wear.
He's soon dressed and clean-shaven, but his hair... it is still a sadness. Much happier now, he wonders if she's some kind of special agent. She tells him she and some others are trying to fix what went wrong with time. "Where's the Roman?" he asks. "You mean Rory, my husband Rory," she says. She shows him one of her sketches. It looks nothing like Rory. It looks like the offspring of Philip J. Fry and Tom Welling, the existence which the barriers of reality and biology had heretofore prohibited. Not surprisingly, she hasn't been able to find him in this reality. Amy wonders if they can't just stay this way, with all of time happening at once. "Time isn't just frozen, it's disintegrating," the Doctor tells her. Time is like so much ice cream left in the freezer for too long. Captain Williams, one of Amy's soldiers, politely interrupts to tell them they've almost arrived. It's Rory, also wearing a patch. The Doctor gives him a big smile but Amy still doesn't recognize him.
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.