Battle of Demons Run

The Battle of Demons Run was the name River Song gave to an attack on the station on Demons Run by the Eleventh Doctor in his effort to rescue Amy Pond and her baby, Melody. River described the confrontation as the Doctor's darkest hour, saying that he would rise higher than ever before and then fall so much further. In its aftermath, River revealed that she was Melody, an identity she had spent a long time hiding from the Doctor.

A day to come
During the crash of the Byzantium, River Song acknowledged whilst speaking with Father Octavian that she was dealing with the Eleventh Doctor at an earlier point in his time stream, before he learned exactly who she was. (TV: The Time of Angels)

Prelude
Madame Kovarian of the Kovarian Chapter made an alliance with the Church. This alliance was known to the Papal Mainframe and their forces included Anglican marines under Colonel Manton and the Order of the Headless. Amy Pond's unborn daughter, Melody, was a vital item in their plan. Kovarian wished for her to become a weapon, calling her hope in an "endless, bitter war" against the Doctor — the Siege of Trenzalore. Amy and Rory Williams conceived Melody while on the Doctor's TARDIS in the time vortex. This gave her the potential to become part Time Lord, with additional experimentation. (TV: A Good Man Goes to War, The Time of the Doctor)

At some point, Amy was taken to Demons Run and replaced with a ganger controlled by her; as far as she and Rory knew, nothing had happened and she was still with the Doctor and Rory. The Doctor, though, realised. After travelling to the 22nd century to see the early stages of the Flesh the ganger was created from, he cancelled the link, destroying the ganger. Amy woke on Demons Run where she gave birth to Melody. (TV: The Rebel Flesh / The Almost People)

The Doctor and Rory were determined to rescue Amy and Melody. They destroyed the Twelfth Cyber Legion to make that point to Amy's captors and blackmail the Cybermen into telling them where she was. The Doctor recruited allies who owed him a debt from across time and space. The Silurian Madame Vastra and her maid and partner Jenny Flint, the Sontaran nurse, Commander Strax and Dorium Maldovar; all came. Rory went to the Stormcage Containment Facility to ask River for help, but she refused, saying she couldn't come until the "very end", as it was the day the Doctor would rise so high and then fall further than ever before. She said it was the day he found out who she was.

At Demons Run, Colonel Manton gave a speech about the Doctor. Amy watched from above, but was interrupted by a cleric, Lorna Bucket, who offered her a prayer leaf with Melody's name on it in the language of her people. Amy ignored the offer, but turned when she realised Lorna had met the Doctor. She accepted the gift and warned Lorna to be "on the right side" for her own sake. (TV: A Good Man Goes to War)

The battle
Lorna hurried to the speech, where Colonel Manton revealed the true nature of the Monks. He removed two of their hoods, revealing knots of skin where the bases of their necks should have been. The third Monk removed his own hood, revealing himself as the Doctor. The Monks raised their swords and the marines (except Lorna) raised their guns. At that moment, Vastra and Jenny captured the control room. The Doctor put up his hood as the lights went out. The lights came back on and the Doctor was nowhere to be seen. He said he was disguised as one of the Monks; his voice echoed and his location couldn't be pinpointed. A marine shot a hooded figure who turned out to be a real Monk.

The Monks killed several marines in retaliation until Colonel Manton ordered his force not to fire. Lorna noticed a Monk using a sonic screwdriver on the door and followed him out of the room while the rest of the marines disarmed themselves on Manton's orders to restore order. When the marines disarmed, an army of Silurians and Judoon led by Commander Strax suddenly appeared with their own weapons pointed at the marines. Strax held the Colonel at gunpoint, claiming the base.

Manton warned he had a fleet which would come to the asteroid if it was taken. However, the Doctor had summoned a group of Dalek Upgraded-Spitfires to disable their communications.

Making her escape, Kovarian ordered Melody brought to her ship, saying that the Doctor must think he was winning until the trap closed. Unknown to her, Lorna was listening, and ran off.

Rory appeared and held Kovarian at sword point; Henry and Toby Avery arrived, and Henry announced her ship was captured. Colonel Manton and Kovarian were both brought to the control room, where the Doctor told the Colonel to tell the marines to "run away". He wanted Manton to be known for the rest of his life as "Colonel Run Away" — a warning to those who would try to use the Doctor's friends to get to him. Madame Kovarian told the Colonel to give the order, even calling him by that nickname, and the clerics were escorted off the station by the Judoon.

The Doctor and Rory united with Amy, presenting her with her baby. Madame Vastra entered and said that the marines were leaving, that not a drop of blood had been spilt and that the Doctor had never risen so high — words Rory remembered from River Song's warning.

Dorium hacked the computers and discovered scans of Melody. They revealed that her DNA contained traces of Time Lord. Vastra asked when Melody was conceived; she knew that the Time Lords had evolved through exposure to the time vortex. The Doctor realised that the first time Amy and Rory were together on the TARDIS (in this version of reality) was their wedding night. Vastra deduced that Amy's kidnappers had wanted a Time Lord for a weapon. When the Doctor asked how a Time Lord could be used as a weapon, Vastra pointed out what he was capable of. Vastra and Dorium left as the Doctor remembered the little girl from 1969 America. Kovarian suddenly appeared on a view screen and said that the girl was hope in the war against the Doctor.

Strax found Lorna eavesdropping and brought her to Rory and Amy. She insisted that they were in a trap and she had joined the clerics only to meet the Doctor, a great warrior. When the lights went out, Strax detected no life forms in the base excluding them and the Silurians. Lorna said that the Headless Monks did not register as life forms as they were not alive.

Elsewhere in the base, the Monks massacred the Silurians. Vastra joined the others; the TARDIS was suddenly surrounded by a force field and the doors were locked. Dorium identified the Monks' chant as the attack prayer. Amy hid with Melody. Dorium went to the Monks, even though he had sold them out to the Doctor. He was beheaded; his body joined the Monks, who advanced on the group. Rory, Vastra, Jenny, Strax and Lorna formed up to protect Amy and Melody. The true Battle of Demons Run began.

Back in the control room, the Doctor told Kovarian that a child is not a weapon. Kovarian smugly told him she would become one. When the Doctor vowed not to let her recapture the child, Kovarian said that fooling the Doctor once was a joy, but fooling him again the same way was a privilege — i.e. Melody was a flesh avatar just like Amy had been discovered to be in the previous episode. In a panic, he ran off to find Amy.

Rory, Vastra, Jenny, Strax and Lorna battled the Headless Monks with guns and swords, while Amy waited, holding Melody; then, she screamed in horror as Melody collapsed into flesh. The Doctor ran onto the scene where the battle had ended, shouting that Melody was flesh; he was greeted by Rory, who told him sullenly that they knew. The Headless Monks were all dead, but Strax and Lorna were both mortally wounded and died shortly afterwards. (TV: A Good Man Goes to War)

Directly after the battle
River Song appeared with a crash of thunder. The Doctor confronted her. The battle, she said, was entirely a result of his actions. She told him that he frightened so many people. Though the word "doctor" often meant healer or wise man, in the Gamma Forests it meant "mighty warrior". The Doctor, fed up with her riddles, finally asked River who she was; she only ran towards his cot. She directed his attention to the cot and asked him to read what was there. His anger turned to joy, and after a few words with River, he returned to the TARDIS with a new-found confidence; he told Amy and Rory not to worry because he knew where Melody was. He told River to return everyone home. Despite Amy's protests, the TARDIS dematerialised.

After the Doctor departed, Amy held River at gunpoint demanding to know what she had told the Doctor. River handed her the prayer leaf and told her to read it. The people of the Gamma Forest didn't have a word for "Pond", because "the only water in the forest is the river". As Amy and Rory read the leaf, the TARDIS translation circuits made the writing change to read "River Song". River was Amy and Rory's daughter. (TV: A Good Man Goes to War)

In the days following
Though he was thought to have been killed by the Headless Monks, Strax woke up two days after the battle, being tended to by Vastra and Jenny who informed him that he had fainted. They invited him back to their own time and Strax accepted the offer. (WC: The Battle of Demon's Run: Two Days Later) He returned to Victorian London with Vastra and Jenny, functioning as their butler and henchman. (TV: The Snowmen)

According to River, the Headless Monks and the Silents cut ties with Kovarian after the battle. (AUDIO: The Furies) While the Silents appeared as if they continued to work with her after the battle, (TV: Closing Time) they were in fact more than willing to betray and kill her for their own ends, as seen in a later aborted timeline. (TV: The Wedding of River Song)

Behind the scenes
According to The Brilliant Book 2012, Ood Sigma was helping the Doctor in his attack on Demon's Run, explaining why Russell T Davies is given credit for creating the Ood in A Good Man Goes to War even though no Ood was seen.