London, 5:02 p.m., 22nd April 2011
Across the city, all times and places co-exist. Steam trains run across a 21st century cityscape while cars float on hot air balloons. Children avoid pterodactyls in the park while a Roman charioteer waits at a stop light. While newspapers proclaim that the War of the roses is going into its second year, Charles Dickens does a television interview talking about his upcoming Christmas special about three ghosts.
Holy Roman Emperor Winston Churchill returns to Buckingham and the Silurian Dr. Malokeh, his personal physician, checks his blood pressure. Churchill glances at the time and then realizes that it's 5:02... and it has always been 5:02. Malokeh doesn't realize there is anything unusual and says that it is already 5:02 p.m. on April 22, but Churchill insists that something is wrong and has his soldiers bring the Soothsayer from the Tower. Once he's alone with the Soothsayer, Churchill demands to know why time is locked at one point and everything is happening at once. The Doctor, aged and bearded and wearing robes, looks up and says that a woman has caused everything.
In the period just before his death, the Doctor finds a Dalek aboard a crashed ship and taps into its data core to find out everything it knows about the Silence. He then goes to the docks of Calisto B and convinces a barman to let him see Father Gideon Vandeleur, the former envoy of the Silence. The eyepatch-wearing Gideon meets with the Doctor, who offers his condolences on the death of the real Gideon. The Time Lord then shorts it out and stares into its eye, and asks to speak with Commander Carter of the Teselecta. He figures that they're posing as Gideon to investigate the Silence and asks Carter what the Silence's weakest link is.
The Doctor then meets with the weakest link, an eyepatched Gantok, and challenges him to a game of live chess. Gantok is soon caught in a lethal checkmate and is unable to move without killing himself. The Doctor offers to concede in return for the information he wants about the Silence. Gantok admits that only Dorium Maldovar has the information the Doctor wants, and will take the Doctor to Dorium if he concedes.
After the Doctor forfeits, Gantok takes him to the tombs of the headless monks, filled with the carnivorous skulls of their many decapitated victims. As they skulls watch them, the Doctor and Gantok go to a box containing Dorium's freshly decapitated head. Gantok tries to double-cross the Doctor and kill him, but he sets off one of the tomb's many traps and plummets into a pit filled with the skulls.
Churchill points out that the Doctor's story is absurd, and the Doctor explains that in another the reality, the two of them were close, giving Churchill the ability to sense something is wrong. The Emperor reminds the Doctor about the woman he mentioned earlier and asks if she's attractive, and the Doctor says that she's hell in high heels.
Dorium tells the Doctor that the Silence consider themselves the sentinels of history and want to eliminate the Doctor. They believe that he will ask the First Question on the Fields of Trenzalore during the Fall of the Eleventh. When the question is answered, Silence must fall, and so the question must not be answered. The Doctor asks Dorium to tell him the First Question and Dorium does so. Once he has the Question, the Doctor takes Dorium's head box to the TARDIS and brings up the file on the death. Dorium insists that now that the Doctor knows the Question, he has to accept that he must die.
The Doctor explains to Churchill that the Silence must eliminate the secret, and they know that the Doctor knows the question. The Doctor's silence must fall so the Question can never be asked. As they talk, Churchill takes the Doctor to the Senate Chamber and is surprised to discover that he's holding a gun. The Doctor looks at his left arm and sees an ink mark on it.
Dorium explains that Lake Silencio, Utah, is a still point in time, making it a perfect site for the Silence to create a fixed point in time: the Doctor's death. The Doctor refuses to accept his death and says that he can keep on dodging the moment forever by traveling to other times and places. As Dorium warns the Doctor that time catches up to everyone, the Doctor decides to call an old friend, Brigadier Lethbridge-Stewart, at the nursing home. He's shocked to learn that his old friend passed away a month ago. Stunned, the Doctor hangs up and then takes out the three blue envelopes from his coat pocket. He then turns to Dorium and admits that it's time.
The Doctor returns to Calisto B and asks Carter and his crew to deliver the envelopes so he won't cross his own timestream. Carter knows that it's the Doctor's dying request and agrees to deliver them. As the Doctor leaves, Carter asks if there is anything else they can do for him but the Doctor goes out the door.
Churchill asks why the Doctor invited his friends to watch him die, and the Time Lord explains that his friends have always been the best part of him... and he couldn't bear to die alone. He then tells Churchill that they're running out of time.
It is April 2, 2011, at 5:02 p.m. The Doctor, River, Rory, and Amy go to Lake Silencio, Canton Delaware arrives, and the impossible astronaut emerges from the lake. The Doctor tells everyone to stay back and not interfere, and then goes to confront the astronaut. The suit's visor opens, revealing River inside. She says that she's a prisoner and can't stop the suit, and the Doctor tells her that she's not supposed to because he has to die. He assures her that she won't remember what happens, and that in the future River will serve out a prison term for murder for a crime she didn't commit. When River says that she can't bear to see him die, the Doctor explains that he wants to her see and hear so that she can know that he has completely forgiven her. The suit fires repeatedly, blasting the Doctor. There's a flash of light and the Doctor realizes that he's still alive. Smiling, River says that fixed points can be rewritten. There's a burst of energy and...
When Churchill wonders what happened, the Doctor explains that because he didn't die as dictated by history, nothing happened... and will always happen, and never stop. Time is frozen at 5:02 p.m. and will start disintegrating. The Doctor suddenly realizes that he's holding a spear and Churchill confirms that he's fired his gun. Realizing what's going on, the Doctor explains that they have been fighting the Silence, and as soon as they lost eye contract, they forgot what happened. The Doctor checks his left arm and is relieved to see there are only four marks... until he looks at his other arm and sees dozens more. They look up and see a horde of the Silence on the ceiling, ready to drop down on them.
Before the Silence can attack, soldiers charge into the room and use a stun grenade to take out the Silence. Amy, wearing an eyepatch, marches into the room and then shoots the Doctor with an electronic stun gun. When he wakes up, the Doctor discovers that he's on a train bound for Cairo. Amy apologizes for stunning him and he assumes that she has forgotten about him in the new reality. However, when he sees all of the sketches she has made of their time together, the Doctor realizes that Amy has remembered. The two friends share a reunion and the Doctor is soon back to his old self. Amy explains that a number of people have realized that time has gone wrong and that they have a plan to deal with it. The Doctor asks what happened to Rory and Amy says that she loves him, but she can't remember who she is. All she has is a sketch she's made of him. She remembers the events of Lake Silencio twice over, with the Doctor both dying and living, and he explains that time has frozen because his death was prevented. Rory comes in, wearing an eyepatch as well, and reports to Amy, his commander. Amy doesn't recognize him and the Doctor figures that she's too close to the issue.
The train arrives at the Area 51 pyramid and Rory gives the Doctor an eyepatch. He explains that it's an I-Drive that communicates directly with the brain, constantly reminding the user of the existence of the Silence. Over a hundred Silence are stored in tanks filled with insulating fluid. As the Doctor passes by, the Silence react to him and Rory tells his men to check the systems. As Amy goes on ahead, the Doctor suggests that Rory ask Amy out on the date and claims that Amy said that Rory was hot. Rory doesn't believe him and suggests that they keep going.
Amy and Rory take the Doctor to the command center. River is wearing an I-Drive as are the rest of the staff, and they have Madame Kovarian prisoner. When the Doctor comes in, River declares her love for him, now and always, but the Doctor says the important thing is to stop the disintegration of time. He to grab her arm and time starts moving again. For a moment they are back at Lake Silencio with the Doctor ready to die at River's hands. Amy has her soldiers pull him away and handcuff him, and the Doctor insists that he has to short out the differential to restart time and stop the disintegration. He and River are opposite poles of the disruption, and touching each other will undo the effect.
One of the Silence starts cracking open its glass cell. Meanwhile, Rory notices insulating fluid leaking through the pyramid. Rory notices, unaware that another of the Silence has already broken out and is closing in on him. In the command center, River is telling the Doctor she doesn't want to murder him, while Amy notices the insulating fluid leaking in and calls out a warning. Kovarian boasts that the Silence was never imprisoned, but have only been waiting for the Doctor arrive.
Rory runs in, bolts the doors, and warns them that the Silence is loose. As they prepare for the attack, Kovarian tells them that the I-Drive they are wearing are based on the one that she's wearing, and that the Silences never give away an advantage. The I-Drives activate on their own, electrocuting several of the staff members. As the others take off the I-Drives, Kovarian realizes that the Silence has activated hers as well. She begs the Doctor for help but he goes to River and Amy and tells them that they are risking the universe to keep him alive. They offer to show him what their plan is and he agrees. As River takes him to the top of the pyramid, Amy tells Rory that he has to remove the I-Drive before it activates. Shaking in agony, he tells her that it already has but that he needs to wear it to fight the Silence, and that she needs to go. Amy thanks him for his sacrifice and leaves.
The Silence break into the control room and Rory collapses in agony. One of the aliens approaches him and says that this time he will die for good and never come back. As it prepares to electrocute him, Amy returns and guns down the Silence. As she leads Rory away, Kovarian asks her for help as her I-Drive comes partially off. Amy refuses, saying that Kovarian stole her child and that she'll never have the chance to see her as a baby, but Kovarian points out that the Amy has to save her because that's what the Doctor would do, and Amy would never do anything to disappoint him. Amy considers the argument and then says that the Doctor isn't there. She places the I-drive on Kovarian's eye and gets Rory out as the woman screams in agony. As they head to the top, Amy suggests that they have a drink and get married.
Atop the pyramid is a temporal distress beacon from the TARDIS. River explains that she has sent a SOS through the bubble of time/space surrounding Earth, simply saying, "The Doctor is dying. Please help." The Doctor doesn't believe it means anything, but River explains that there are millions of entities waiting outside the bubble, all there to do whatever they can. She reminds him of all the good that he's done and the people that he's helped that he's forgotten. The Doctor insists that he still has to die but River refuses to let him die because of her love for him no matter what it will cost the universe.
Amy and Rory arrive and the Doctor asks Amy to uncuff him. He then wraps one end of his tie around his hand and the other around River's, and tells Amy and Rory to perform a brief marriage ceremony. As they do so, the Doctor whispers something in her ear and tells her that she has to remember it but never tell anyone. As River stares in surprise at what she's heard, the Doctor tells her that it's his name. He then asks her to become his wife but then end his life because he can't bear the guilt of the universe's destruction. River agrees, learning forward to kiss him, and time starts up.
At Lake Silencio, the Doctor dies at River's hands and the timestream returns to normal.
Sometimes later, River travels through time for a point just after she left the Byzantium to see Amy. Amy is guilty about leaving Kovarian to die, even though technically it never happened because that timestream never occurred. She'd like to talk out her guilt with the Doctor but can't, and River tells her that the Doctor isn't really dead. Amy initially assumes that she means that River can see the Doctor as she travels backward through time, but River then explains that the Doctor didn't tell her his name atop the pyramid, but something else. A few minutes later, Rory comes out and finds his wife and daughter hugging and dancing on the lawn. As they tell him about the Doctor, Amy realizes that she's now the Time Lord's mother-in-law.
A hooded figure brings Dorium back to the tomb and opens the box. As he turns to go, Dorium realizes that it's the Doctor and asks how he escaped. The Doctor throws off his robe and explains that the Teselecta crew had their ship take on his form. When River looked into "his" eyes during the marriage ceremony, she saw the miniaturized Doctor inside, waving to her and then gesturing for her not to say anything. Everything happened at Lake Silencio exactly as it appeared. Now the Doctor plans to stay in the shadows since he's been too noisy and endangered too many of his friends. Dorium points out that River will be in prison for a crime she didn't commit, but the Doctor notes that she will only serve her time during the day... and her nights with him.
As the Doctor walks away, Dorium calls out that it will all still happen: the Fields of Trenzalore, the Fall of the Eleventh, and the asking of the Final Question, the question hidden in plain sight, the question that can never be answered that the Doctor has run from all his life. As the Doctor goes to the TARDIS, Dorium calls out the question: "Doctor Who?"