On a distant junk planet, Auntie brings a woman, Idris, to Uncle. He says that its time as their Ood servant escorts Idris to a chair. When Idris asks what will happen, Auntie explains that her mind will be drained and her body will be left empty, but Idris will soon have a new soul. As the Ood, Nephew, forces Idris down, Auntie says that a Time Lord is coming.
The Doctor is regaling Rory with stories of his past adventures when the warning lights come on. As the Doctor checks on them, Rory warns Amy yet again that they can’t talk about seeing the Doctor’s death, even though it won’t happen for two hundred years of the Doctor’s personal time. There’s a knock on the TARDIS door even though they’re in deep space. The Doctor hesitantly opens the doors and finds a small electronic box outside. It soars inside and he grabs it, and explains that it’s mail. As he sets the coordinates, he explains to Rory and Amy that the box is a Time Lord mailing system, and the tattoo on it belongs to the Corsair, a “good” Time Lord who had the tattoo in every incarnation. When Amy points out he’s the last Time Lord in the universe, the Doctor says that they’re going to a different universe. He starts jettisoning TARDIS rooms to get the necessary power and takes the ship into a bubble universe where they’ve never been. The power goes out and the Doctor says that it’s impossible. He tells his companions that the matrix, the soul of the TARDIS, has vanished.
In the junkyard, a golden light enters Idris accompanied by the sound of a TARDIS materializing, and Idris looks at her glowing hands with awe.
The Doctor, Amy, and Rory emerge from the TARDIS, and the Doctor admits that he doesn’t know what happened to his friend. They confirm that the TARDIS has been drained of almost all energy, but the Doctor believes it will refuel from all the rift energy in the bubble universe. Idris, Auntie, and Uncle come running up and Idris immediately kisses the Doctor. She then calls him a thief, saying he has stolen her and is stealing her. Auntie and Uncle introduce themselves and explain that Idris is off her head. Uncle says that Idris bites, and she immediately bites the Doctor’s ear. She says he’ll be angry because the little boxes will make him angry. She rants and predicts that Rory will ask a question, and then collapses. Uncle says that she’s dead but Rory confirms that she’s still breathing. Uncle tells Nephew to take Idris somewhere that she can’t bite.
The Doctor takes notice of Nephew and explains to Rory and Amy that it’s harmless, and then offers to repair its broken translation sphere. He fixes it and they hear a transmission of the Corsair’s distress signal, intended for the Time Lords, filled with voices. Nephew shuts it down and the Doctor says that it’s not a transmission, but something else, something not possible. Shocked, the Doctor demands to know who else is there. Auntie insists that there is no one else there except House, which surrounds all of them and is the entire world. She offers to introduce House to the Doctor and the Doctor agrees. As they go, the Doctor tells his companions that the other voices were those of Time Lords. Somewhere close by are lots and lots of Time Lords.
Nephew locks Idris up in a cage, and when she wakes up she talks of sadness, in the past, present, and future tense.
Auntie and Uncle take the trio to their main living area, and the Doctor realizes that the asteroid is sentient. House speaks through both Auntie and Uncle, welcoming the newcomers. It knows the Doctor as a time traveler and says that it repairs people that come through the rift. House says that it has encountered Time Lords and TARDISes in the past, but there are none there now. The Doctor tells it that there won’t be any more because he is the last. House invites them to stay, rest, and eat, and the Doctor accepts its invitation. Auntie and Uncle snap out of their trances, and Auntie strokes Amy, saying that House loves them.
In her cage, Idris rants to herself and then wonders why she’s saying what she’s saying. She screams and the Doctor faintly hears her.
As they explore, the Doctor says that they have to find the other Time Lords, and Amy realizes that he wants to explain and get forgiveness for wiping out the rest of his kind. He asks her to go to the TARDIS to get his sonic screwdriver, and Amy agrees but warns him not to get emotional because that’s when he makes mistakes. She leaves, telling Rory to look after the Doctor. The Doctor tells Rory to go with Amy to look after her, and Rory goes after his wife. They enter the TARDIS and close the doors, unaware of a green mist springing up around the base. Once inside, Amy calls the Doctor to confirm that the sonic screwdriver is in his other jacket. He tells them to have a good look, activates the sonic screwdriver that he had all along, and the TARDIS doors lock shut.
The Doctor begins looking for his fellow Time Lords and finds a cupboard filled with the electronic mail boxes. Each one is emitting a message of distress from a Time Lord. Uncle and Auntie come up behind the Doctor, who congratulates them on their collection. He turns on them and asks how House repairs them, and points out that Uncle has mismatched eyes and two left feet, literally. Auntie has a man’s arm with the Corsair’s snake tattoo on it, and the Doctor warns that they gave him hope and took it away. He tells them to run and they do, but not before Uncle warns that House is too clever.
Amy calls and says that they haven’t found his sonic screwdriver, and the Doctor admits that he got them out of the way. The Doctor realizes that Idris knew he would find the boxes and become angry. He tells Amy and Rory to stay put and then goes to confront Idris.
In the TARDIS, the green mist rises up over the TARDIS exterior. Inside, Amy complains that the Doctor doesn’t trust them and that it’s bad. Rory notices a green glow starting to enter through the doors and says that it probably is.
The Doctor asks who Idris is and she says that he should know her. She explains that they put “her” inside of Idris, and that she travels with the Doctor. Idris makes the dematerialization noise and the Doctor realizes that the TARDIS consciousness is inside of the woman. He doesn’t believe it at first, but Idris describes how they first met, and how the Doctor stole her. Idris suggests that he now release her and he does, and she explains that House eats TARDISes. Seeing the Doctor’s future conversation, she recites his explanation that House can’t eat a TARDIS without blowing a hole in the universe, so it downloads the TARDIS matrixes into a human receptor
Realizing what is happening, the Doctor calls Amy and Rory and tells them to get out. They’re unable to get out even though the Doctor has unlocked the door. As the Cloister Bell starts ringing, the Doctor gets to the TARDIS shell and tries to open the doors by snapping his fingers, but nothing happens. The cell phone goes dead and Amy asks Rory to hold her hand. The TARDIS dematerializes and the Doctor is unable to call them, and he realizes he has no idea what to do.
When Amy worries, Rory says that they’re in the TARDIS and they’re safe. House speaks up, saying that he’s half right and they are in the TARDIS. It says that it is going on a great adventure and asks why it shouldn’t kill them now.
The Doctor returns to Idris and the others, and Auntie explains that they’re dying and it’s time for them to go. When the Doctor said his was the last TARDIS, House realizes that there would be no more “food” arriving and took the TARDIS into the primary universe. First Auntie and then Uncle collapse, and Idris says they have to go, now. As she leaves, she clutches at her side and asks how long the bodies last. The Doctor scans her and confirms that she’s dying, but Idris tells him to focus. He wonders what he can do in a junkyard, but then realizes that it’s a TARDIS junkyard. As he starts to leave, the Doctor asks what he can call her, and Idris tells him to call her Sexy, just like he does in private.
House starts to fill the TARDIS with his consciousness, and then asks them again why he should keep them alive. Amy turns to Rory, who finally explains that killing them immediately wouldn’t be fun, and it kept Auntie and Uncle alive to make them suffer. House tells them to entertain it, orders them to run, and they do.
The Doctor scans the junkyard and finds the abandoned TARDIS shells left by House. Idris realizes that the Doctor plans to build a working TARDIS out of the scavenged remains despite the fact it’s impossible, and the Doctor says that as long as they’re alive, nothing is impossible.
Amy and Rory run through the TARDIS corridors and House taunts them. They almost fall down a shaft and House explains that it has shut off the corridor anti-grav.
As the Doctor gathers parts, Idris complains that he never follows instructions and has been pushing rather than pulling the TARDIS doors for over seven hundred years. He complains that she’s not very reliable, and Idris says that she always took him where he needed to go. Switching tracks, the Doctor says it would be great if they could talk all the time. Idris says it isn’t possible and wavers, warning that one of the kidneys have already failed and she has 18 minutes left.
House closes a door in the corridor, separating Amy from Rory. As she tries to go back, Amy hears a voice calling to her. She walks around a corner and finds Rory, who explains that she’s been gone for hours. Amy realizes that House is messing with the TARDIS interior configuration and they start running. Another door closes, separating them.
The Doctor and Idris assemble a makeshift console room with a Time Rotor. As they work, Idris explains that she left herself unlocked because she wanted to see the universe. The Doctor finishes the work, give or take a few pieces.
Amy moves down the corridor and finds an elderly Rory, who accuses her of leaving him. He says that “they” come for him every night and hurt him, and asks how Amy could have left him for that. A door closes, cutting them off.
The Doctor and Idris put on safety belts and try to start up their TARDIS. There’s no power to start it up and the Doctor admits they have nothing. Idris tells him that he has what he’s always had: her. She kisses her fingers, creating a spark of energy, and touches the makeshift Time Rotor. It lights up and they depart in pursuit of the Doctor’s TARDIS.
Amy walks down the darkened corridors and finds the walls covered in blood graffiti, vows to kill her. She finds Rory’s wizened corpse and screams in horror. As she apologizes, Rory comes up behind her, his proper age, and the illusion of the graffiti and words disappear. They embrace and realize that House is messing with their heads.
The Doctor flies the new TARDIS toward the rift and locks onto his TARDIS. He asks Idris to send a telepathic message to Amy. She’s not sure which one is Amy.
As they climb through the TARDIS, Rory gets Idris’ telepathic message. She tells him to go to the old control room and lower the shields so they can phase inside, and they have 10 seconds to do it and get out. Rory tells Amy about the message and they continue climbing. Meanwhile, Idris explains that even though the Doctor has deleted the old control rooms, she has archived them, including the future ones he hasn’t deleted yet.
As Amy and Rory head to the control room, Amy suddenly finds herself in darkness. Rory can see and warns that House is messing with their heads again, and he sees a light up ahead. He tells Amy to stay put and goes to investigate, and there’s a scream. After a second he says that he’s fine and just banged his head. Amy stumbles blindly forward and touches Nephew. Rory finds her and they run away. They get to the control room and Idris sends Rory a telepathic passkey to open the door. He recites the words but nothing happens, and Amy realizes that since it’s a telepathic interface, they have to think it. As Nephew approaches, Amy visualizes the feeling behind the words and the door opens. They get inside into the Ninth and Tenth Doctor’s old control room and Rory drops the shields.
Idris realizes that they’ve succeeded.
House asks Rory and Amy how they found the control room and then lets Nephew in. As the Ood advances on them, Idris telepathically contacts Rory and tells him to get out of the way, but doesn’t say where they’re coming through. Rory tells Amy to hang on as the makeshift TARDIS appears in the control room. The Doctor introduces the weakening Idris to his companions, explaining that she’s his TARDIS. House orders Nephew to kill them, and they realize that it was redistributed into the airs when the new TARDIS arrived.
House admits that he didn’t expect the Doctor, and demonstrates all the ways that it could dispose of him and the others. The Doctor says that it can’t because it needs his help, because the TARDIS doesn’t have enough power for House to escape the bubble universe through the rift. He asks House for its word that it will spare them, assuring Amy that the creature is an entity of its word. Idris is burning up from fever and the Doctor tells her to hold on. House promises to spare them and the Doctor tells it to burn up 30% of the TARDIS rooms to provide necessary propulsive force and gives it the proper subroutine. The creature realizes that it can delete the control room and rid itself of them all, and activates the subroutine.
The TARDIS appears in the primary universe and the Doctor, Amy, Rory, and Idris materialize in the current control room. The Doctor explains that anything in a deleted room automatically appears in the main control room. House asks why it shouldn’t kill them anyway and tells them to fear it because it has killed Time Lords. The Doctor points out that he killed all the Time Lords, but then admits that House is a worthy opponent and has everyone applaud. Rory says that Idris has stopped bleeding, and the Doctor notes that House ripped a TARDIS consciousness out of its matrix so it would burn out away from the control room. When House wonders why it makes a difference, the Doctor says it should have been careful what it put back in the control room. The TARDIS matrix energy emerges from Idris and fills the room, and House tells the Doctor to make it stop. The Doctor tells the TARDIS to finish off House and it screams in agony.
The TARDIS speaks through Idris one last time, saying that it has finally found a big complicated word that is so sad, and it has found it. It tells the Doctor that the word is “alive,” and it is alive, but now that time has ended. It says that it’s been very, very nice to meet him and then Idris’ body disappears.
Later, the Doctor makes sure that everything is working. Amy asks if he’ll make the TARDIS talk again, and the Doctor reluctantly admits that he can’t. Rory says that as Idris was dying, she said one thing over and over. “The only water in the forest is the river.” The Doctor figures that they’ll need to know it someday, and asks Rory if he’s okay. Rory admits that he watched Idris died and couldn’t do anything, and the Doctor tells him that being alive now is what matters. As he prepares the TARDIS to depart, Amy says that ultimately it’s just the Doctor and the TARDIS, long after the rest of them are gone. The Doctor says that’s the best thing there is, and then offers to make them a new bedroom since House deleted the old one. He reluctantly agrees not to give them a bunk bed this time. Once they leave, the Doctor goes to the console and asks if she can hear him. He gets no response, but the TARDIS activates on its own and laughing, the Doctor watches his ship depart.