Amy

After The Doctor and Rory Williams discover that Amy Pond has been taken from them, and had been replaced with a doppelganger made from ‘The Flesh’ (see "The Rebel Flesh/The Almost People"), they are determined to find Amy and her baby.

The Doctor having learnt that the real Amy is being held on a secret asteroid base called Demon’s Run, calls in some old debts so bringing together several old allies, including a Sontaran nurse called Commander Strax, Silurian Madame Vastra and her human companion Jenny Flint, and the black market trader Dorium Maldovar. With their help he plans to lay an assault on the base. Meanwhile, Rory, after collecting information on the base's location from a Cyberman fleet, attempts to bring River Song from her prison cell, but she claims that she cannot be with The Doctor at this time, as this battle is when he will discover her true identity.

Aboard the supposedly secret base, Madame Kovarian, who has been watching over Amy during her pregnancy and has taken her child, Melody Pond, from her, prepares her human troops to fight The Doctor. Alongside the human troops are members of the Order of the Headless Monks who reside at Demon’s Run. Meanwhile human soldier Lorna Bucket, who had met The Doctor as a young girl in the Gamma Forests, attempts to befriend Amy, but Amy warns her of The Doctor’s fury if she fights against him. Before Lorna Bucket leaves she gives Amy a good luck token – a piece of cloth that she had embroidered Melody Pond’s name on it.

Rory Meets the Cybermen

As Colonel Manton shows the troops that the hooded Headless Monks are, literally, headless and thus cannot be influenced by feelings, The Doctor disguised as a Headless Monk, appears to their surprise. Then when all the lights go out, plunging the hanger into darkness, The Doctor is able to slip away to continue with his plan to rescue her baby. The Doctor though is followed by Lorna Bucket who, on losing him, overhears Madame Kovarian, who is about to leave the base with Amy’s baby, stating that The Doctor must continue to think that he is winning until the trap closes.

Meanwhile on the hanger The Doctor has left behind confusion as the human soldiers start firing on the Headless Monks, believing one of them is The Doctor. The Monks retaliate and a battle rages until Colonel Manton regains control by ordering the powering down of all weapons. Then assisted by additional Silurian, Sontaran, and Judoon forces, along with space-worthy Spitfires (see "Victory of the Daleks") and Captain Avery and his crew (see "The Curse of the Black Spot"), The Doctor and his allies secure the base and defeat the human troops. They also free Amy, and retake Melody before Madame Kovarian can escape with her.

Madame Kovarian

As The Doctor celebrates, as it is consider that this is his greatest achievement, Madame Vastra and Dorium discover that Madame Kovarian had been scanning Melody Pond and had found traces of Time Lord DNA in her. The Doctor surmises that Amy’s baby was likely to have been conceived on Amy and Rory’s honeymoon aboard the TARDIS resulting in the baby’s DNA being influenced by the time vortex.

While the rest of The Doctor’s allies regroup, Amy and Rory tend to their daughter using an ancient wooden cot that The Doctor claims was his own. The Doctor also confirms to Amy that even though her heart and mind was on the TARDIS physically she has spent all her time, while pregnant, as Madame Kovarian’s prisoner on Demon’s Run and that she was abducted before the recent events in America. The Doctor then returns to a control room, in an attempt to find some answers as to why Amy was abducted, and what Madame Kovarian wants with Amy’s baby. But then Madame Kovarian, well away from the base, contacts The Doctor, explaining that they will be using Melody Pond as a weapon in the war against him. She then takes delight in telling The Doctor that he has fallen into another trap, and that fooling him twice is a privilege.

Realising what she means The Doctor races to the main hanger but already the TARDIS has been blocked by a force field, and his allies are being attacked by the Headless Monks, who kill Dorium, Commander Strax and Lorna Bucket before they are defeated.

Rory with Commander Strax

While the battle rages Madame Kovarian, appeares through a hatch opening in midair near where Amy and Melody are hiding and tells the baby to wake up. To Amy’s horror her baby dissolves into liquid Flesh. This sends Amy into hysterics.

As they recover from the recent deaths and the shock revelation that Madame Kovarian still has Melody, River Song appears to the group through a teleportation device. At first The Doctor accosts her for not helping them, but she tries to explain that she could not. She also tells The Doctor how these recent events were brought about by those who feared The Doctor. The Doctor, who is still very angry, demands to know who she is.

To answer his question River Song shows The Doctor the cot, directing him towards what appears to be some Gallifreyan symbols on its side. The Doctor eventually comes to a revelation, silently recognising River Songs’ identity to himself. Elated, he goes off on his own in the TARDIS to rescue Melody, asking River Song to return everyone to their homes.

Dorium

Still shocked by the loss of her baby, and with the sudden departure of The Doctor, Amy uses a discarded gun, that she picks up from the floor, to force River Song to explain what The Doctor learned. River Song shows them the cot. Initially Amy believes River Song is referring to the Gallifreyan symbols on the side, but they cannot be read by humans. Instead River Song shows her what lies within the cot. It is the cloth token that Lorna Bucket had given Amy with Melody Pond’s name on it.

As Amy looks at the cloth the strange symbols translate into the words ‘River Song’. Seeing that Amy requires further explanation, River Song reveals that as the Gamma Forest people do not have a word for ‘Pond’, Lorna Bucket used the closest approximation which is ‘River’.

River Song then announces, to a stunned Amy and Rory, ‘It's me. I am Melody. I'm your daughter’…