On the Demon's run military base, Amy is looking after her baby daughter, Melody Pond. Madame Kovarian, the Eye Patch Lady has come to take the baby. Amy tells Melody that her father is coming for them.

On one of the ships of the Twelfth Cyber Legion, the Cybermen detect an intruder working his way up the levels of the ship. It is the Last Centurion (aka Rory Pond). He tells them that the Cybermen monitor everything in the quadrant and therefore he has a question and the Doctor has a message. The question is, "Where is my wife?" The Cyber leader asks what the Doctor's message is. Behind Rory, in space, the ships of the fleet begin to explode. Rory asks if he needs to repeat the question.

On Demon's Run, two Clerics (the Fat Man and the Thin Man) pass Lorna Bucket, another soldier. They are talking about the Doctor destroying the Cyber Legion and the time he drove the Atraxi from the Earth. They ask Lorna about her encounter with the Doctor. The Fat Man leaves with three Headless monks to complete a conversion tutorial. The Thin Man stays with Lorna, to talk about the Doctor. She says she met him when she was a young girl in the Gamma Forest, and he told her to run. The Fat Man is brought to the Headless Monks' headquarters and is asked to make a donation. The Monks advance on him with an empty box. He realises that they are going to take his head.

In Victorian London, a hooded figure returns home. She tells her maid, Jenny, that she has just defeated Jack the Ripper, and eaten him. She is the Silurian woman, Madame Vastra. Jenny shows Vastra to the drawing room, where the TARDIS waits. Vastra says that a very old debt is about to be repaid. She tells Jenny to pack the swords.

In the Battle of Zaruthstra in 4037, Commander Harcourt needs a nurse to tend the son of the President. A Sontaran, Commander Strax, enters and tends the wounded boy. As he leaves, Strax says that he was made a nurse as a penance. He hears the TARDIS nearby and says that his penance may be finished.

River Song returns to Storm Cage Containment Facility. She has been on a birthday outing with the Doctor. Rory steps out of the shadows, still in his centurion outfit. Rory tells River the Doctor needs her and that she must come with him. River checks her diary and calculates that it is the Battle of Demon's Run. She says that she can't be there until the very end. She tells Rory that this is the day when the Doctor will rise higher than ever before, and then fall so much further. It is also the day when he finally finds out who she is.

Dorium Maldovar, entrepreneur and bar owner of the Maldovarium, is packing to leave. Madame Kovarian and Colonel Manton stop by to interrogate him. They say that they have already waited a month and the Doctor has done nothing. Dorium tells them that the Doctor is raising an army of people who owe him a debt. He also knows that the Clerics and the Headless Monks are based on an asteroid called Demons Run and adds that the name comes from an old saying: "Demons run when a good man goes to war." Kovarian and Manton leave, thinking that there is nothing to be learned. As soon as they have gone, the TARDIS materialises. Dorium is horrified to realise that he has been recruited, too. He protests that he is old, fat and blue.

At Demon's Run, Colonel Manton makes a speech to the military, both Clerics and Monks. He tells them that the Doctor is just a man and they must not believe the stories they've heard. Amy watches all of this from her room, above. Lorna comes in to give her the prayer leaf she has sewn with Melody's name in the language of her people. Amy initially ignores the offer until she realizes that Lorna has met the Doctor. S takes the leaf but tells Lorna to be on the right side when the Doctor arrives.

Lorna arrives at the speech as Manton is telling the Clerics that he has received a dispensation from the Papal mainframe that will allow him to lower the hoods of the monks so that they can see why the monks are invincible. As he lowers the third hood, the monk is revealed as the Doctor. The Monks brandish their swords and the Clerics raise their guns at him. Up in the control room above, Vastra and Jenny overpower two guards and turn off the lights in the hangar. The Doctor puts his hood on and tells Amy to get her coat. The lights come back on and the soldiers look at the Monks to see which the Doctor is. One of the Clerics panics and shoots a Monk. The Monks retaliate and a battle seems about to begin.

Colonel Manton orders the Clerics not to fire as he removes his weapon pack and drops his gun. The other Clerics do the same. Lorna sees a Monk using a sonic screwdriver to unlock a door and follows him. An army of Silurians and Judoon materialise on the walkways and hangar floor. The Clerics realise they are beaten. Commander Strax appears and holds a gun to Manton, telling him that Demon's Run is taken. Manton says that he will call in the fleet but the Doctor has a squadron of Spitfires attack the communications array.

Kovarian escapes towards her ship, accompanied by two Clerics carrying Melody in a cot. Kovarian sends the Clerics back to the hangar, telling them that it is important the Doctor thinks he is winning until the trap closes. Lorna overhears all of this from the shadows. She runs away but Rory appears and confronts Kovarian. She asks him how he plans to take her ship with twenty of her crew aboard but the doors open and Henry Avery and his son, Toby, appear: the ship is theirs.

Kovarian and Manton are taken to the Doctor in the control room. The Doctor tells Manton to order his men to run away; he wants Manton to be made infamous for those words and known as Captain Runaway for the rest of his life. The Doctor is angry and doesn't want anyone to use his friends to get to him again. Rory brings Melody to Amy in her room. Their tearful reunion is interrupted by the Doctor and meets Melody; the Doctor reveals that he can speak baby. Madame Vastra comes in to say that the Judoon have departed with the Clerics. It is only when she announces that the Doctor has never risen higher that Rory remembers River's words.

The victors gather in the hangar. Amy says that Melody is crying because the TARDIS noise bothers her. They discuss whether she needs feeding or changing but the Doctor brings a cot from the TARDIS , saying the baby is tired. Rory and Amy wonder why Amy was kidnapped and why the Clerics and Madame Kovarian wanted possession of Melody. Amy asks the Doctor what he thinks is happening, but he changes the subject and tells her that the cot was his. He goes to the control room where Dorium has gained access to Kovarian's computer files. He finds some scans of Melody's DNA, which show traces of Time Lord DNA. Vastra wonders where and when Melody was conceived. She knows that Time Lords only achieved their status through exposure to the time vortex and the Untempered Schism. the Doctor recalls that the first time Amy and Rory were together on the TARDIS after he rebooted the universe was on their wedding night. He thinks back to Amy's worries that her baby would have a 'time head'. Vastra suggests that Kovarian wants Melody as a weapon. The Doctor wonders why a Time Lord would be a weapon but Vastra reminds him of the things he has done. Dorium reflects that the Clerics' were beaten too easily and that something is wrong. The Doctor reconsiders what he has learned: the little girl from 1969 America with super-human strength, enough to escape from the astronaut suit. Kovarian appears on a screen in the control room. She tells the Doctor that Melody is "hope" in their war against the Doctor.

Back in the hangar, Lorna is brought in at gunpoint by Strax. She warns the group that she overheard Kovarian talking of a trap. They say that this is what they would expect a Cleric to say but she tells them she only joined the Clerics to meet the Doctor. She calls him "great warrior." Amy says that the Doctor is not a warrior, so Lorna asks why he is called "the Doctor" in that case. The lights in the hangar go off. Strax checks for life forms in the base other than the group around him and the Silurians: the result is negative. However, Lorna says the Headless Monks aren't alive and won't register. The Monks attack the Silurians and a force field surrounds the TARDIS as the doors in the hangar begin to lock. Dorium identifies the Monks' chant as "the attack prayer". He goes forward to greet them, saying that the Monks know him of old but he is beheaded. His headless body joins the Monks as they close in on the Doctor's friends. Rory leads Amy and Melody away into the shadows behind some crates and then joins the others as the battle begins.

The Doctor, up in the control room, tells Kovarian that Melody is not a weapon and he will never let her near Melody again. Kovarian drily replies that fooling him once was "a joy," but fooling him "twice in the same way - it is a privilege". He rushes off to Amy.

As the fighting goes on, Melody sees a hatch open, apparently in mid-air, and Kovarian whispering "Wakey wakey." Melody dissolves into Flesh, and Amy screams Rory's name. The Doctor arrives after the battle is ended and Rory says that they know Melody is Flesh. The Headless Monks have lost or withdrawn, Lorna and Strax have been mortally wounded. Strax informs Rory that dying is not the pleasure he thought it would be but he reflects on a long life - after all, he is twelve. The Doctor tries to give some comfort to Amy but she is too distraught to have anything to do with him. Vastra takes him, instead, to Lorna. She says that they met before but she does not think he will remember her. The Doctor lies, saying he remembers everyone and that they ran together. He asks Vastra who she was. The Silurian cannot tell him but remarks that she was very brave.

The Doctor, dejected, comments that they were always brave. He turns to leave but River Song appears in the hangar. The Doctor wants to know why she did not come earlier, when he asked her. River says that she could not have prevented any of it happening the way it did but suggests that the Doctor could. She asks if this is how he imagined events would unfold when he first set out on his journeys: a man who could turn an army around at the mention of his name. She points out that the word 'Doctor' means 'healer' or 'wise man' in much of the universe but 'great warrior' in the language of the Gamma Forest. The Doctor demands to know for once and for all who she is. She says that she is telling him now and glances at his cot. He reads the Gallifreyan carving and his face changes to delight. He looks with amusement at Amy and Rory before abruptly entering the TARDIS. He calls back to Amy to say that Melody is safe and then takes off.

Amy picks up a pistol and points it at River, demanding to know what she said to the Doctor. River hand the prayer leaf to her that Lorna sewed, which was in the cot. She says it is Melody's name in the language of the people of the Gamma Forest but they don't have a word for "Pond," because "the only water in the forest is the river." The TARDIS translation matrix gradually takes effect and the stitching on the prayer leaf changes from Melody Pond to River Song. River smiles, saying that she is their daughter. Amy and Rory gaze at her in disbelief.

Rory drive's his Mini erratically through a wheat field with Amy in the passenger seat shouting intricate instructions. They screech to a halt in front of the TARDIS with the Doctor brandishing a newspaper - the Leadworth Chronicle. It shows an aerial photograph on the front page of the crop circles they have just made, spelling out the word "doctor". Rory tells him this is because he never picks up his phone. Rory notices a line through the word that they did not make. Another car drives across the field towards them and the Doctor dives out of its way. It halts suddenly and Amy and Rory's friend Mels gets out. She is delighted to see the TARDIS at last and knows who the Doctor is. As police sirens are heard she produces a gun and tells the Doctor she needs to get away. She suggests they us the TARDIS and the gun to kill Hitler.

In a montage of shots, Mels repeatedly gets into trouble: at primary school for insulting a teacher because she has never heard of the Doctor; at secondary school for the same thing; in a police station for stealing a bus. Finally, in Amy's bedroom, she manages to point out to Amy that Rory has not got a girlfriend because he loves Amy and not (as Amy has assumed) because he is gay.

The TARDIS spins, out of control, through the sky. Mels has shot the console to test out the "clever lie" that weapons don't work in there because the TARDIS is in a state of temporal grace.

In 1938 Berlin, a Nazi officer, Erich Zimmerman, enters his office, watched by a workman wearing overalls. Inside the workman is a crew of tiny people who gather data on the officer's appearance. One of the tiny crew makes her way to the eyeball and looks out because she doesn't trust the sensors (they "made Rasputin green" apparently). On the way she has to update her privileges on a wristband to prevent the anti-bodies (robotic jellyfish in appearance) from killing her. The workman (actually the Teselecta) assumes the shape and size of Zimmerman who is shrunk and beamed aboard where he is left to the antibodies to be exterminated.

The Teselecta enters Hitler's office and begins the process of sentencing and punishing him for his war crimes. However, one of them points out that it is 1938 and too early in his time stream; they need to return later.

The TARDIS crashes in through the window. Hitler dives under his desk and the Teselecta is knocked out. The Doctor staggers out of the TARDIS, followed by the other three. He tells them not to re-enter because of a cloud of toxic smoke caused by Mels having shot the console. Hitler thanks them for saving his life and asks what the blue box is. The Doctor says it is a police box from London and "The British are coming." The Teselecta stands up and Hitler produces a gun and fires at it several times. Rory punches him and then, on the Doctor's instructions, locks him in a cupboard. The bullets missed the Teselecta but hit Mels in the stomach. The Teselecta scans the TARDIS and says that they have found an even bigger war criminal than Hitler.

Mels reveals that she is Melody Pond (apparently Amy named her daughter after her best friend who was her daughter all along) and regenerates into the woman they know as River Song. She runs around excitedly checking out her new body while the crew of the Teselecta confirm that they have got the woman who kills the Doctor in their clutches. River produces a gun and tries to shoot the Doctor but he had previously removed the bullets. She pulls another gun, only to find he has swapped it for a banana. As she produces a knife and another gun (both proving futile) she explains that she was programmed for this assassination when she was a child. Eventually she seems to relent and kisses the Doctor before exiting through the window to go shopping. As she leaves she reveals that this was her actual method of execution. The Doctor collapses, dying, and the Teselecta scan reveals to its crew that he has been poisoned. The Doctor tells Amy and Rory to go after her. They arrive at ground level as a party of six soldiers shoot her but River uses her regenerative energy to knock them down and, laughing, steals their guns and a motorcycle.

The Teselecta arrives on a motorbike and Amy and Rory knock it off and steal the bike. Rory says he expects he will be able to ride the bike because it is that sort of day. The Teselecta changes form to incorporate a motorbike and sets off in pursuit. Its crew wonder how the Doctor can die here and now when the records show that his death is known to be at Lake Silencio in 2011.

The Doctor falls into the TARDIS and asks for a voice interface. It appears first in the form of a hologram of the Doctor. He asks for someone that he likes instead and it changes to Rose Tyler, Martha Jones and Donna Noble. He rejects each because of the guilt he feels at seeing them. Finally, it becomes young Amelia Pond. The Doctor tries to get it to help him but it replies that he has been poisoned and has 32 minutes to live. It adds that the poison came from the Judas Tree, there is no cure and that regeneration is impossible. He pleads for something to inspire him and it mentions "Fish fingers and custard." He laughs and drags himself over to the console.

Melody arrives at a restaurant and threatens the diners with a machine gun. She steals all of their clothes and sends them out. Amy and Rory arrive, followed by the Teselecta, which has now assumed the form of Amy. The Teselecta enters and accuses her of killing the Doctor on the orders of the movement known as The Silence and the Academy of the Question.

Amy and Rory find themselves inside the Teselecta. the antibodies threaten them but one of the crew gives them wristbands and tells them that they are aboard Justice Department Vehicle 6018.

The TARDIS arrives in the restaurant and the Doctor steps out in top hat and tails. He uses a sonic cane to deduce that the Teselecta is a justice machine with 423 people miniaturised to fit inside. Amy sends him a signal, using the sonic screwdriver, to show that she and Rory are in there, too. The Teselecta explains that it travels to criminals near the ends of their lives in order to "give them hell." By this it means that they are put into a state of perpetual pain. As a demonstration it envelopes River in an energy field and tortures her. The Doctor, now collapsed due to kidney failure, begs them to stop. The Teselecta says that time travel has responsibilities; the Doctor retorts that going back to torture dead people doesn't seem very productive.

The Doctor demands to know who arranged his death. Amy tells the Teselecta captain that the Doctor is her best friend and that River is her daughter. She says she has a right to know what is happening. She is given access to the records department and tells the Doctor that the Silence, a religious movement, believe "silence will fall" when the Oldest Question in the Universe is asked. It says that Question is hidden in plain sight but does not know what the Question actually is.

The Doctor pleads with Amy to stop the Teselecta torturing River. She uses the sonic screwdriver to destroy the crew's security clearance wristbands, provoking the antibodies into an attack. The captain asks the mother ship to teleport to them away, leaving only Amy and Rory aboard. The Doctor, with only three minutes to live, begs River to save her parents. She is impressed by the fact that he still cares about others in his last moments and demands to know who 'River' is.

Amy and Rory embrace as the antibodies close in on them but the TARDIS materialises around them. They look to see the Doctor but find it is River who has flown the TARDIS. She says that the Doctor told her she is the child of the TARDIS and the TARDIS taught her how to fly it. They go back into the restaurant and find the Doctor in his last moment. He tells Amy and Rory that there is no way for him to survive. He asks to speak to Melody and tells her to find River Song. He whispers something in her ear and she replies that she is sure "she already knows". The Doctor's consciousness fades and she asks Amy who River Song is. Amy asks the Teselecta to show them River Song and it changes form to become River. Melody asks her parents if the Doctor is "worth it". They say she is and River kisses the Doctor, passing her regenerative energy into him.

This obviously has a debilitating effect for she wakes up in a hospital bed. Amy tells her that she shouldn't have used up all of her remaining regenerations to save the Doctor, whereas he gives her the diary that she will use later to keep track of their meetings.

In the TARDIS, the Doctor looks at some information he downloaded from the Teselecta: the day of his death. He keeps this hidden from Amy, saying only that he has left River in the best hospital in the universe in the care of The Sisters of the Infinite Schism and that one day River will find her way back to them. Amy asks how River will do this.

River applies for a degree in Archaeology at the Luna University in 5123. When the professor asks her why she wants to do this she replies that she is "looking for a good man."