At a lab aboard a floating asteroid base, Demon’s Run, Amy picks up her baby, Melody, while the Eye Patch Lady, Madame Kovarian, steps forward with a squad of soldiers. Amy assures her daughter that the Doctor is on his way.
Twenty thousand light years away, a figure sabotages the 12th Cyberlegion’s base, causing chaos.
Madame Kovarian steps forward and takes Melody from Amy, while the soldiers and a group of monks look on.
The Cybermen detect an intruder.
As the baby is placed in a containment pod, Amy assures Melody that her father, the Last Centurion, will find her no matter what.
The Cyberleader and his men confront the intruder... Rory. He says that he has a message from the Doctor and his own question. Rory demands to know where his wife can be found, pointing out they monitor the entire region. The Cyberleader asks what the Doctor’s message is, and Rory simply waits as the Cyberships floating in space outside the station blow up. He then asks the Cyberleader if he has to repeat his question.
A short time later at Demon’s Run, the soldiers learn that the Doctor destroyed a Cyberlegion just to make a point. One of the soldiers, Lorna Bucket, is stitching lettering into a piece of cloth. Her fellow soldiers, Lucas and Dominicus, go to the monitor room and keep an eye out, while complaining that they’ve been on yellow alert for three weeks.
Two Headless Monks make their way through the base. Two gay soldiers, Thin One and Fat One, wonder why they’re called Headless when they have heads. Lorna, overhearing them, explains that the monks follow their hearts, not their heads. As three of the monks arrive to take Fat One goes to a conversion class, Thin One realizes that Lorna had an encounter with the Doctor and asks what he was like. She says that she met him as a child, and when she encountered him, he only said, “Run.” Lorna explains that she’s from the Gamma Forests despite the fact that it’s neutral.
The Headless Monks lead Fat One to a conversion chamber, and a tannoy voice tells him that visiting armies offer their soldiers for conversion. The Monks approach him with a box and ask if he’s ready to make a donation.
Thin One wonders where the Doctor is, and Lorna notes that he could be anywhere in time and space.
In London, 1888, a robed woman returns to her home and tells her maid, Jenny, to send a message to Scotland Yard that Jack the Ripper has claimed his last victim. The woman places a Japanese katana back in its rack and removes her hood to reveal a Silurian. The maid, unsurprised, says that something has come up in the drawing room. The Silurian, Madame Vastra, enters and finds the TARDIS. She tells Jenny that it means that an old debt is to be repaid, and that she should prepare the swords.
At the Battle of Zarusthara in 4037 A.D., Captain Harcourt and Eleanor are tending to an injured boy, Lucas. A Sontaran comes in and introduces himself as a nurse, and tends to Lucas. Once he confirms that Lucas is okay, the Sontaran, Strax, says that he’ll live to die another day in glorious battle against the Sontarans. As Strax leaves, Harcourt asks how he came to be a nurse, and Strax tells him that he’s serving penance for the honor of his clone-batch, and helping the weak and sick is the greatest punishment a Sontaran can endure. As he goes out, Strax hears the sound of the TARDIS materializing and tells Harcourt that his penance may be at an end. He tells Harcourt to get some rest until he crushes the life from him and then goes to the nearby TARDIS.
River Song breaks in to Stormgate Prison and calls the authorities to turn off the alarms since she’s returning. As she dances down the hallway, she sees Rory in his Legionnaire uniform. Surprised, she explains that the Doctor took her ice skating for her birthday, on the Thames in 1814, and had Stevie Wonder sing for her. She tells Rory never to tell his Doctor that, and checks her diary to confirm that it’s Demon’s Run. He tells River that they’ve taken Amy and his baby, and they’re going after the people responsible. The Doctor wants River, but she says that she can’t, not yet. When Rory asks why, River explains that it’s the Battle of Demon’s Run, the site of the Doctor’s greatest victory and most crushing defeat. She tells Rory that she can’t be there until the very end, because it’s the day when the Doctor finds out who she really is.
On a distant planet, bar owner and merchant Dorium Maldovar is packing to leave when Madame Kovarian and her soldiers arrive and she asks what he’s heard. Dorium tells her that he’s learned that she’s angered the Doctor and he plans to be far away. When Kovarian notes that it’s been a month and nothing has happened, Dorium warns that the Doctor will call in the debts of people that owe him. Her lieutenant, Colonel Manton, doesn’t believe it, but Dorium warns him that God help the people that owe the Doctor, and the ones he plans to turn them loose against. Manton and Kovarian dismiss Dorium’s concerns, but as they go, he tells them that their base is called Demon’s Run because of the legends that say Demon’s Run is where a good man goes to war. Kovarian and Manton leave without comment as Dorium chuckles.
As Dorium completes his preparations to leave, he hears the TARDIS materializing. It appears before him and the door opens. As Dorium yells that he’s too old and fat to be of any help, the Doctor’s silhouette falls on the wall behind him.
At Demon’s Run, Manton addresses his soldiers while the Headless Monks look on. Manton tells his men that the Doctor is a living, breathing man, and they’ll put an end to that. Amy watches them through the observation portal in her room. Lorna comes in and apologizes for being there instead of at the rally. She gives Amy the piece of cloth she was working on earlier, a prayer leaf with Melody’s name stitched on it in the language of her people. Lorna tells Amy that as long as she holds it, her child will always come back to her. Amy casually asks for her gun so she can stop Lorna from talking. When Lorna doesn’t hand it over, Amy comments that Manton is talking like the Doctor is famous, but she insists that he isn’t. Lorna explains that the Doctor meets a lot of people and they remember, and he’s a dark legend. She tells Amy that she met the Doctor when she was a little girl, and Amy says that’s when she met the Doctor as well. Lorna figures that Amy must be very special, and Amy tells Lorna that the Doctor will come, and Lorna should be sure and be on the right side when he arrives, for her own sake. Amy takes the prayer leaf and thanks her and Lorna leaves.
Manton continues his rallying speech as Lorna arrives in her place. The colonel explains that they’ve allied themselves with the Headless Monks. As Thin One looks around for his mate, Manton says it’s time for the soldiers to learn what the Headless Monks have sacrificed for their faith. Three of the Monks step forward and Manton explains that the Papal Mainframe has granted permission for them to lower their hoods. He lowers their hoods and reveals that they have no heads, and can never be persuaded or surprised. The next monk lowers his hood on his own and reveals that he’s the Doctor. The Monks and soldiers draw their weapons
In the monitor room, Vastra and Jenny capture Lucas and Dominicus.
Manton tells the Doctor to surrender, but the Doctor ignores him and calls out to Amy, telling her to get her coat. The lights go out momentarily. When they come back up, the Doctor has disappeared. He calls out, saying he’s one of the Monks. The soldiers panic and one shoots a Monk, and the Monks return fire until Manton gets everyone to cease firing. Lorna notices a Monk near the door using a sonic screwdriver to open the lock.
Vastra casually dismisses all mammals, offending Jenny. As they quibble, Lucas tries to get to the door-locking mechanism, but Vastra strings him unconscious.
The disguised Doctor gets through the door and Lorna goes after him. Meanwhile, Manton disarms his weapon as a gesture of good faith and tells the soldiers and Monks to do the same. As they do so, Vastra and Jenny watch on the monitors and wonder where the Doctor is.
Lorna finds the Doctor’s discarded robes.
The soldiers and Monks finish disarming, and platoons of Silurian and Jadoon warriors teleport in, led by Commander Strax. Manton warns that the fleet will attack when an automatic distress signal goes off. The Doctor comes on the tannoy and announces he has a fleet of his own. A squadron of space-going British RAF Spitifres open fire on Demon’s Run, destroying the communication array and preventing Manton from sending his signal.
Kovarian tells her two soldiers to get the child so they can evacuate. Once they get it, they go to her ship and she tells them to go with the others, and that the Doctor must think he’s winning right until the trap closes. As they run off, Lorna listens from the shadows and leaves. Rory arrives and draws a sword on Kovarian, and she asks how he plans to defeat her crew of 20. Captain Henry Avery and his son Toby emerge and say that the ship is theirs.
Strax escorts Manton to the monitor room, and the Doctor tells the colonel to order his men to “run away.” In fact, he wants Manton to be remembered by those words, so that others won’t consider trying to get to the Doctor through those he loves. When Kovarian is brought in, she says that anger isn’t an issue for a good man, because they have too many rules. The Doctor warns her that he’s not a good man, and to not try and find out why he has so many. Kovarian tells Manton to give the order.
As Rory opens the door to Amy’s chamber, she tells him that they took their baby. He comes in holding Melody and assures her that will never happen. Rory breaks into tears and admits he’d hoped to be cool, but Amy assures him that he is. The Doctor comes in as they kiss and starts to retreat, but Rory tells him to come in and meet their daughter. Vastra arrives and directs their attention to the soldiers, who are retreating without any blood spilled. She talks of how the Doctor has never risen higher, and Rory remembers what River said earlier.
Amy and Rory take Melody to the TARDIS, but the baby is upset by the noise. As they step outside, Jenny and Strax inform them that everything is being restored to normal. The Doctor brings out a very old crib. They wonder if he’s ever had children, but the Doctor dodges their questions. He’s called to the control room, and tells Amy and Rory that they can’t leave until they know what the base was for. When Amy wonders if she was in the TARDIS, the Doctor gives her a hug and explains that physically she was at Demon’s Run, and that a Flesh avatar of her was with them since before America and their encounter with The Silence. The Doctor notes that whoever beamed the control signal for the avatar into the TARDIS is very clever, and Rory wonders if there’s anything he’s not telling them. In response, the Doctor admits that he couldn’t say anything about the Amy avatar because he wasn’t sure if “they” might be listening. As he turns to go, Amy asks him to answer one thing. The Doctor says that it’s his…cot. As the Doctor leaves, Strax finds Lorna, listening at the door, and brings her in.
In the control room, Dorium is tapping the computers. Vastra is there and comments on the Doctor’s early anger, and warns that it can lead to mistakes. He had given her the same advice when he found her killing tunnel diggers as revenge upon her sisters. Vastra then asks if the baby is human, and Dorium reveals that the computer files confirm that Melody had both human and Time Lord DNA.
Lorna explains that she heard Kovarian said that she was preparing a trap. She only joined the army to meet the Doctor again, and that she only joined the army so that she could meet a great warrior. The lights go out and Lorna warns that it’s starting.
Vastra notes that Time Lords gained mutated DNA over exposure to the Untempered Schism, but the Doctor insists it only occurred after millions of years. She wonders if Melody could regenerate, and the Doctor admits that he isn’t sure. When Vastra asks when they might have conceived a child, the Doctor admits that the first time Amy and Rory were married and had a chance was on their wedding night... in the TARDIS.
Strax detects no life signs, but Lorna warns that the Headless Monks aren’t alive.
Dorium suggests that Manton and his men gave in too easily, and figures that something is wrong. The Doctor wonders why Kovarian would want a baby Time Lord, and Vastra suggests it could be used as a weapon. She agrees with Dorium and says that they have to get back with the others. As the two of them go, the Doctor remembers what they learned when scanning the child in the spacesuit. Kovarian transmits a signal, assuring the Doctor that she’s far away, and tells him that the child is hope in an endless, bitter war... against the Doctor.
The Headless Monks arrive in the cargo bay, kill the Silurian troops, and surround the TARDIS in a force field. As Vastra and Dorium arrive, the doors lock behind them. They hear the attack prayer and prepare to fight, while Rory hides Amy. He kisses Amy and Melody and then goes back to fight with the others.
As the Doctor’s allies gather what weapons they can, Dorium suggests that they negotiate with the Monks instead. He goes to meet them and they decapitate him and move in.
Kovarian assures the Doctor that Melody will become a weapon, given time. When the Doctor says he won’t let them anywhere near Melody, Kovarian boasts that they’ve fooled him twice. He realizes what she means and runs to the cargo bay.
Amy tries to comfort her crying daughter while energy blasts and screams fill the cargo bay. She’s unaware that Kovarian is watching her and Melody on a hidden monitor. Meanwhile, the others fight a desperate battle against overwhelming odds, and Strax and Lorna are brought down. Kovarian gives a command word to the baby, and it dissolves, revealing itself as a Flesh avatar. As Amy calls to Rory, the Doctor arrives at the locked door to the cargo bay and tries to warn them. He opens the door and comes in, and Rory tells him that they already know. Rory goes to the dying Strax and tries to comfort him, saying that as a warrior, he’ll recover. Strax tells him that he’s a nurse.
The Doctor goes to Amy, who believes it was all for nothing. He tries to hug her but she backs away. When Jenny says it’s not the Doctor’s fault, Amy admits that she knows but still walks away with Rory. Vastra tells the Doctor that the dying Lorna wants to talk to him. He thanks her for helping his friends, and Lorna tells him that she met him once as a child. Lorna figures that he doesn’t remember her, but the Doctor assures her that he does, and that they ran, the two of them. Lorna dies and the Doctor asks Vastra who she was, and Vastra says that whoever she was, she was very brave. She asks what they should do next, and concludes that they will have taken Melody to Earth to raise her in the correct environment. The Doctor agrees with her, but concedes that it’s too late.
There’s a flash of light and River appears. The Doctor angrily asks where she’s been, and River says that she couldn’t have prevented what happened. When she blames the Doctor, he denies that it was his fault, but River says that he makes people afraid, and that he’s come a long way from being a healer and a wise man. Now they consider him a mighty warrior. The Doctor demands to know who she is, and she puts his hand on the crib and tells him to read the symbols. When he does, the Doctor looks at her in surprise and then smiles, introduces himself to River, and giggles. Overjoyed, he realizes what her being alive means and asks how he looks.
The Doctor tells Amy and Rory that Melody will be safe, and asks River to get the others home. He deactivates the force field around the TARDIS, enters it, and departs before Rory and Amy get enter. They turn to River and asks where he is going, and Amy draws a gun. River tells Rory that everything is fine, and that the TARDIS translation matrix takes a while to kick in for written words. She tells Amy to concentrate, but Amy can’t read the writing on the crib. River says that it’s Gallifreyan, which doesn’t translate, but hands her the prayer leaf inside of the crib. Amy concentrates on it as River says that explains that the Gamma Forest people don’t have a word for “Pond,” and the only water in the forest is a river. As River tells Amy and Rory that she knows the Doctor will find and protect their daughter no matter what it takes, Amy concentrates and the Gamma Forest words “Pond Melody” translate for her... into the words “River Song.” River tells them that she’s Melody, their daughter.