Earlier; a dying Dalek sees the Doctor approach. He takes from it everything that it knows about the Silence. This leads him to the docks of Calisto B where he tracks down Father Gideon Vandaleur, former envoy of the Silence. The Father is exposed as the Teselecta but the crew sends him on to find Gantok, another of the Silence's agents. Gantok plays a game of live chess with the Doctor (meaning they play with live electricity). Gantok is facing checkmate (and death unless the Doctor forfeits the game). The Doctor agrees to forfeit if Gantok can tell him why he has to die. Gantok says that he will take the Doctor to Dorium Maldovar's head where he will get the answers. So, in the seventh transept of the Headless Monks, the Doctor and Gantok find Maldovar's head in a box. Gantok tries to double-cross the Doctor and produces a gun. However, the ground falls away beneath his feet and he plunges into a pit filled with living skulls that devour him.
The Doctor asks Dorium about the Silence and is told that they are a religious order of great power who consider themselves the guardians of history. Dorium says that the Doctor's future terrifies the Silence. He says that "On the fields of Trenzalor, at the fall of the Eleventh, when no creature can speak falsely or fail to answer, a question that must never be answered will be asked: the first question, hidden in plain sight." He asks if the Doctor wants to know what this question is. The Doctor nods. He takes Dorium's head with him into the TARDIS. Dorium protests at being taken but also says that the Doctor now knows the question.
Back in the senate room, Churchill asks the Doctor what the question is. The Doctor replies with a question: what would Churchill do if he knew that a man could speak a secret so devastating that it would threaten everything? He adds that he had never realised that it was his silence that was spoken of in the prophecy, or his death. They look around the room and wonder how they got there or why Churchill is holding his revolver. The Doctor looks at his arm which has a single pen stroke on it. He carries on with his story.
In the TARDIS, Dorium says that Lake Silencio in Utah is a still point in time and therefore easier to create a fixed point - the Doctor's death. The Doctor says he will not go to his death yet but intends to continue his farewell tour. However, when he phones his old friend the Brigadier to come with him, he finds that the Brigadier has died. He realises that the time has come. He finds the Teselecta again and asks it to deliver the blue envelopes containing the invitations to Lake Silencio. As he leaves the room, the Teselecta asks if there is anything it can do for him. The Doctor leaves in silence.
In the senate room, Churchill asks why the Doctor took his friends to his death. He says that his friends have always been the best of him. Looking at his arm he sees there are now three pen strokes.
At Lake Silencio the Doctor, Amy Pond, Rory Williams and River Song drink a bottle of wine that Napoleon once threw at the Doctor. An astronaut rises from the lake and the Doctor goes to meet it. It is River Song, in the suit created by Madame Kovarian and the Silence. River says that she cannot control the suit and it raises its arm. He tells her that he forgives her and shuts his eyes. Instead of the three shots that kill him there are five and the Doctor is still alive. He demands to know what she has done. River tells him she has drained the weapons system.
The Doctor tells Churchill that nothing happened or, rather, everything happened at once and is continuing to happen. As they discuss this they notice that Churchill's gun has been fired and the Doctor is now holding a sword. They realise that they have been defending themselves and the Doctor's arm is full of tally marks. They look up to see the ceiling is infested with dozens of Silents. A grenade rolls into the hall and soldiers storm in pointing weapons at the enemy. Leading them is Amy Pond. The Doctor is delighted to see her until he realises that she is wearing an eye patch. She raises a gun and shoots the Doctor.
He wakes in Amy's office on a train. She tells him that the effects of the stun gun will wear off soon. He tries to persuade her that they were once friends but as he looks around her office he sees a model TARDIS and drawings of the people and monsters that they have met; due to her time travel and the crack in her wall she can remember both timelines. However, she cannot remember that Rory is the Captain Williams in her detachment of soldiers.
As the train enters Area 52, in the pyramid of Giza, the Doctor tells Amy that his being alive means that time has stopped and, like an explosion, the effect will keep spreading out into the universe until everything falls apart. In the pyramid, the Doctor and Amy walk past tanks of water containing captured Silents. Rory tells the Doctor to put on the eye patch he has been given. All of the soldiers are wearing them, too. Amy explains that it is an eye drive, an external memory that allows people to remember the Silents after they have stopped looking at them.
Rory is disconcerted that the Silents are more active now that the Doctor is in the base. He says that there are more than a hundred of them in the tanks. He sends two men to check the tank seals. The Doctor goes after Rory to try a bit of matchmaking between him and Amy. He then rejoins Amy in the King's Chamber where River Song is waiting. Madame Kovarian is also there, a prisoner tied to a chair. It was her eye patch that was used to create Eye Drives.
The Doctor and River flirt with each other but for him it is a ruse to touch her. He goes to take River's hand and time starts to move again. For a brief moment the two of them are back at Lake Silencio but when they are pulled apart they are back in the pyramid. She has the soldiers put him in handcuffs and tries to persuade him to live. The Silents release themselves from the tanks and start to kill the soldiers. They attack the eye drives, causing death or debilitating agony. Kovarian laughs at them until her eye drive begins to electrify. She begs the Silents to spare her but they tell her (telepathically?) that she is no longer needed. Amy and River beg the Doctor to come with them where they have something to show him. Rory valiantly stays to hold off the Silents. He is overcome when his eye drive electrifies and the Silents taunt him that Amy will never come for him. Amy re-enters with a machine gun and kills all of the Silents before vindictively replacing Kovarian's eye drive so that she, too, can die.
At the top of the Great Pyramid, River has built a time beacon, broadcasting to the universe at all times, future and past. It tells everyone that,"the Doctor is dying, please help." Millions of replies are saying, "Yes, of course". The Doctor, however, continues to insist that he must die to prevent all of time disintegrating. River says that she will suffer more than anything in the universe if he dies without realising that he is loved. The Doctor tells Amy to take off the handcuffs and uses his bow tie as part of a marriage ceremony. Rory tells Amy that he doesn't know what is going on and she explains that in another timeline they had a daughter and she grew up to be River. The Doctor whispers into River's ear and tells her she must never tell anyone what he has just told her. He adds, for her parents' benefit, that he just told her his name.She is astonished at this. He then asks for her help and they kiss. Time begins to move again, River shoots the Doctor at Lake Silencio and the timeline is restored. The balloon cars, pterodactyls and other anachronisms vanish.
Later, Amy is sitting in her garden. River arrives from the crash of the Byzantium and they share a bottle of wine. Amy is still distressed about killing Kovarian but River tells her that all of those events were in an aborted timeline. Amy says that she needs to talk to the Doctor but he is dead. River does not agree. When Amy says that River might be having adventures with him before his death but he is still dead to her, River tells her a secret. Rory finds his wife and daughter celebrating until it dawns on Amy that she is the Doctor's mother-in-law.
A hooded figure replaces Dorium's head in the Seventh Transept. Dorium senses that the figure is the Doctor and asks how he escaped. The Doctor tells him that he was on the beach but inside the Teselecta. He didn't whisper his name to River at their wedding, he told her to look into his eyes where she saw the real Doctor waving at her from inside the Teselecta. He says that he was barely singed by the fire at his funeral. He adds that he has been too noisy and now the universe believes he is dead he can step back into the shadows. As he leaves, Dorium calls after him. The Doctor stands at the doors of the TARDIS while Dorium repeats the question that the Doctor has been running from his entire life. It is, of course, "Doctor who?