Amy is floating in space, still wearing her night dress and dressing gown. The Doctor is holding onto her legs in the open TARDIS doorway. She is delighting in the sight of the Universe as Starship UK comes into view. It looks like a giant city floating through space, each of its vast towers carrying the name of an English county. The Doctor pulls Amy back in and tells her that solar flares burnt the Earth's surface in the 29th Century and the world's population was forced to leave until things cooled down. They land in the ship among a street scene that is reminiscent of 1950s London. On the monitor they see Mandy crying while everyone else moves around her seemingly oblivious to her distress. The Doctor tells Amy that their role is as observers only and they must not interfere. As Amy responds to him she sees that the Doctor has already left the TARDIS and is talking to the girl. Amy follows him out.
She looks around her at London Market. The Doctor asks her what she notices and then supplies his own answer: this is a state controlled with rigid authoritarianism and a population afraid to break from conformity. He cites the public's reluctance to speak to a crying child and the wide berth they give to the Smilers in their cabinets. Then he places a glass of water onto the floor for a moment. They are observed by a hooded figure who phones a man called Hawthorne. Hawthorne in turn phones a woman whose face is obscured by a mask made of porcelain. He tells her that there has been a sighting of someone looking at a glass of water. She says that she will check the screens to see what is going on. Her floor is covered with glasses of water.
As Mandy moves off, the Doctor tells Amy to follow. He tells her to ask Mandy about the Smilers in the booths. She tracks her to a side street where the road is blocked by a striped tent, the sort that covers up road works. Amy wants to go inside to see what is happening but Mandy appears and says there is a hole in the road. She says that the Smilers will not allow anyone to talk about it. She says that they are not supposed to discuss either the Smilers or Below. They discuss Amy's Scottish accent: it seems that the Scots did not join Starship UK but have their own ship. Amy enters the tent and neither of them see the nearby Smiler turn to a frown and then to a grimace of anger. Inside, Amy sees a large tentacle writhing about. It threatens her and she escapes from the tent, only to be surrounded by four hooded men who knock her out with gas.
The Doctor is carrying on his own investigation in the ship's quieter zone. He is surprised that the ducts are not connected. He sees a glass of water on the floor. He meets the woman in the mask. She seems to be following her own course of investigation and asks him what he sees in the glass. He says that there is no engine vibration. He shows her the dummy power couplings and suggests that there is no engine. She says that they are on an impossible ship and there is a darkness that threatens them all. Sh gives him a tracking device that will help him to trace Amy. She says that her name is Liz 10.
Amy finds herself waking up inside a voting booth. The automated booth scans her and gives her age as 1306. Her marital status is unknown. It then shows her a video message from a civil servant that tells her she is going to learn the truth about the spaceship. After that she will be given a choice: forget what she has learned or protest about it. He adds that protesting could have terrible consequences for all. She watches an information film and selects the Forget option. Her memories are wiped. She is then shown a film she recorded in the booth earlier where she tells herself to stop the Doctor from trying to find out what is happening and get him off the ship.
The Doctor arrives in the booth with Mandy. After surveying the technology on display he deduces that she has forgotten the last twenty minutes of her life. The machine performs a scan on the Doctor and concludes that he is not human. This is news to Amy. She says that he looks human to which the Doctor responds that she looks Time Lord. He tells her that he is the last of his race after a 'bad day'. He examines the machine and then presses the Protest button to see what will happen. The floor opens up and both of them tumble down a chute. Mandy is locked out and turns, delighted to see Liz 10, who she clearly recognises. The Doctor and Amy land in what appears to be a garbage pit where they find it difficult to stay on their feet. The Doctor explains that this is because the floor is actually the tongue of a large animal. He presumes that the protestors are delivered to the monster as food.
He uses his screwdriver to make the creature vomit them out and they arrive in a tube where there is a door accompanied by a Forget button. They decide not to press the button. Two Smilers sit in nearby booths. The Doctor asks what is going on. The Smilers leave their nearby booths and approach them. Liz 10 arrives (with Mandy) at the same moment and uses her gun to render the Smilers immobile. As they run through the ship she tells them that she can do what she likes because she is 'the bloody Queen'. Apparently, Liz 10 is short for Queen Elizabeth the Tenth. She also claims to know who the Doctor is because she was brought up on all the stories of his meetings with her family.
The Doctor says that the tentacle that Amy saw must be a part of the same creature whose tongue they stood on. Liz 10 tells them that she has been on the hunt for the creature since her coronation ten years earlier. Somebody is feeding her subjects to it. She takes them back to her residence. She says that her real age is fifty but she looks far younger due to her doctors slowing her body clock. She feels that there is a conspiracy against her among her government. The porcelain mask that she wears is to hide her identity while she is out investigating. It attracts the Doctor's attention. He comments on the fact that it fits so well it can stay on her face by itself.
Cloaked figures close in on them. Each man's human face rotates to reveal a Smiler alter ego. One of the men contacts his superior to let him know that the queen has made a breakthrough in her investigation. Secret plans are set in motion. One of the men tells her that she is to be taken to the Tower on the highest authority. Liz says that she is the highest authority and he agrees with her.
The Doctor, Liz, Mandy and Amy are brought to the bowels of the ship - the Tower of London - where Hawthorne explains that the Beast will not eat the children that it is fed. The Doctor then goes on to show Starship UK has no engines, thus there was no vibration for either the Doctor or the queen to find with their glasses of water. Instead, the ship is powered by a captured Star Whale. The creature's brain is exposed and bombarded with lasers. The agony which ensues makes the creature swim on through space. Both Liz 10 and the Doctor are outraged and the queen orders the release of the whale. Hawthorne says that he is only following orders. Liz also demands that her subjects are not fed to the whale.
The Doctor produces a surprising piece of information. He says that Liz has been the ruler of Starship UK for centuries: her mask is that old and was clearly made for her. He says that she only thinks it has been ten years because every ten years she discovers the truth about the Space Whale and then chooses to forget. If the whale were to be set free then it would mean death for all of her subjects. Hawthorne confirms this idea, adding that he and the Smilers work for her, and shows a video tape of Liz explaining this to herself. In the tape she recalls the horror of children screaming in pain when the solar flares arrived on Earth. She goes on to say that the Star Whale - the last of its kind - came at that time, was captured and used to power the ship. Liz 10 has two choices: buttons marked Forget and Abdicate. The latter will free the whale and destroy the ship.
The Doctor uses his sonic screwdriver to relay the screams of agony that the star Whale emits when it is tortured. He says that the only solution is to destroy its conscious mind so that it can continue to keep the humans alive but not feel the pain. He launches a tirade against humanity and everyone who ever pressed the Forget button. He includes Amy in this. In fact, she comes in for the worst of this vitriol because he suspects she pressed Forget so that he wouldn't find out the truth and arrive at this appalling choice. He ends by telling her that he is taking her home as a punishment and ending her time on the TARDIS.
While the Doctor is preparing for his terrible act, Amy looks about her. She sees that the tentacles which threatened her, and other adults, do not have the same menace for children. Mandy and Timmy are able to stroke them if they wish. She makes Liz press the Abdicate button. Instead of the expected catastrophe the ship lurches and then carries on running calmly. The torture has stopped but the whale continues to power the ship voluntarily. In fact, Hawthorne reports, they are speeding up.
Amy says that she realised that a creature that was very old and the last of its kind could not bear to stand by and watch children cry. The Doctor realises that she is talking about him as much as the whale. They go up onto an observation deck where the Doctor says that she could have killed everyone. She says that she recognised the whale's kindness because she had seen it before. Having come to this reconciliation, they return to the TARDIS. Amy feels she needs to tell the Doctor about her impending wedding when the TARDIS phone rings. Amy answers it and is surprised to find that it is Winston Churchill asking for the Doctor's help. The TARDIS dematerialises to go to Churchill's aid and the Star Whale continues to pilot the Starship UK through the cosmos. There is a large crack in the side of the ship, one that closely resembles the crack in Amy's bedroom.