Oh, of course not! The Doctor and company appear in the main control room. Because there's a safety protocol that ensures that if a room is deleted when occupied by any living beings, those beings are transported to the main control room. House doesn't think it matters what room the Doctor is in when he kills them: "Fear me. I've killed hundreds of Time Lords." Doctor: "Fear me. I've killed all of them." And now it's time for the TARDIS matrix to leave Sexy's body and retake its home in the control room. Which means that House must die. All of this is accompanied by a big speech from the Doctor, but it's the one really overblown part of this episode, just repeating what we're seeing with our own eyes, so I shan't transcribe it.
After the glowy sparks stop flying around and House stops shouting, Sexy's body has disappeared from the ground. And her body, or a reasonable facsimile thereof, is floating just above the floor, speaking to the Doctor. She finally remembers that big, complicated, sad word she's been looking for all episode. That word is "alive." The Doctor tells her that alive isn't sad. TARDIS: "It is when it's over. I'll always be here, but this is when we talked. And now even that has come to an end. There's something I didn't get to say to you." Doctor: "Goodbye?" TARDIS: "No. I just wanted to say hello. Hello, Doctor. It's so very, very nice to meet you." And then her body glows and is gone. And the time when they talked is over. Commercials.
The Doctor is fiddling around with all the cables under the console. And he's wearing some steam-punk looking goggles that are giving me dirty thoughts. Anyway, Amy asks him if he's going to make the TARDIS talk again. He says that he can't, and Rory asks why not. Amy suggests that the answer will be "spacey-wacey." The Doctor attempts a technical explanation, and then just tells them that it is "spacey-wacey" in order to get Rory to stop mucking about with cables that cause sparky explosions. Rory also passes on a message that Sexy kept muttering when she was on the ground: "The only water in the forest is the river." The Doctor allows as how that doesn't make sense right now, but I'm guessing it will in eight or nine episodes. He's talking to the TARDIS as he's making repairs, and Amy notes, "Look at you pair. It's always you and her, isn't it, long after the rest of us are gone." The Doctor noted that House deleted all the bedrooms, and asks the two of them if they wouldn't like a new bedroom. Rory and Amy whisper to each other, and then Amy asks if they can please have a bedroom without bunk beds this time. Like any child, the Doctor is genuinely mystified why anyone wouldn't want a bunk bed. As they leave to find their new room, Rory asks the Doctor if he's got a room. But the Doctor ignores the question, and Amy pulls Rory off before he can press the point.