Rory calls the Doctor over to Sexy, who is burning up. I mean, she's not on fire. But her body temperature is very high. The Doctor calls her "old girl," which she likes very much. House gives his word that he won't kill them, and the Doctor tells him that the key to making it back to the main universe is to delete 30% of the remaining rooms, which will increase thrust. House decides that he can delete rooms and free himself of some pesky passengers if he deletes the old control room. There's a bright light, the control room disappears, and we see the TARDIS make it back through the rift into the our universe. Well, I guess that means that House won, and the series is over.
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.