War against the Doctor

What Madame Kovarian described as an "endless, bitter war" was waged against the Eleventh Doctor by the Kovarian Chapter.

Origins
At the end of the Last Great Time War, the planet Gallifrey, whilst besieged by the Daleks, was transported to a parallel pocket universe by the first thirteen incarnations of the Doctor, resulting in the vast majority of the Dalek Fleet inadvertently destroying themselves in an inferno which the universe observed to be the extinction of both the Daleks and the Time Lords. (TV: The Day of the Doctor)

From their pocket universe, the Time Lords found a crack in time, located on the planet Trenzalore, and broadcast a message through it to the universe through all of time and space. The message, "Doctor who?", became the oldest question in the universe and was intended for the Doctor to respond by giving his true name, confirming to the Time Lords that they had found the right universe and that it would be safe to come through.

The Papal Mainframe arrived at Trenzalore, recognising the significance of the message, created a force field around the planet to protect the small village there. By the time the Eleventh Doctor arrived, hundreds of ships had gathered, including those of the Daleks, who had established a new paradigm after barely surviving the Time War. Tasha Lem, Mother Superious of the Papal Mainframe and friend of the Doctor, assisted the Eleventh Doctor and Clara Oswald in reaching the planet. When the broadcast was revealed to be "Doctor who?", the Doctor refused to leave the planet to be destroyed by his enemies in space, all of whom would seek the destruction of the Time Lords. However, he also was not willing to bring the Time Lords back through the crack, fearing that the Time War would start anew. Initiating the Siege of Trenzalore, Tasha Lem changed the faith of the Papal Mainframe into the Church of Silence so as to ensure that the Doctor did not say his name and restart the Time War. The Kovarian Chapter, represented by Madame Kovarian, broke away from the Papal Mainframe, travelled back along the Doctor's timeline to change history so that he never reached Trenzalore. (TV: The Time of the Doctor)

The destruction of the TARDIS
On 26 June, 2010, the Kovarian Chapter caused the Doctor's TARDIS to explode on Earth, causing a total event collapse which threatened to erase all of reality from history. Shortly following his regeneration, the Eleventh Doctor had discovered cracks in time, "scar tissue" which was later determined to have been caused by the explosion. (TV: The Pandorica Opens) As the eye of the storm, the Earth outlasted the rest of the universe, and was ultimately where the Doctor initiated Big Bang Two, restoring the universe. (TV: The Big Bang)

Melody Pond
The Eleventh Doctor's companions, Amy Pond and Rory Williams, conceived a child on their wedding night aboard the TARDIS whilst it was in flight through the Time Vortex. (TV: A Good Man Goes to War) Amy remained unaware that she was pregnant for a while, (TV: The Almost People) and continued enjoying her honeymoon. (TV: A Christmas Carol)

Amy was secretly replaced with a living flesh doppelgänger during or shortly after her honeymoon. The ganger functioned as an avatar through which Amy perceived existence as if she was present in place of the Ganger. (TV: The Almost People) In reality, Amy was taken to a church marine base on the Demons Run asteroid in the 52nd century to gestate her child, who she would name Melody Pond. Through some combination of the circumstances of her conception in the vortex, plus interference by the Silence, Melody developed Time Lord characteristics, including regeneration. (TV: A Good Man Goes To War)

Whilst travelling with the Doctor and Rory in Ganger form, Amy caught some glimpses of the unfamiliar Madame Kovarian observing her on Demons Run, (TV: Day of the Moon, The Curse of the Black Spot, The Rebel Flesh), but remained unaware that she had been kidnapped. The Doctor, however, did become aware of her replacement, and travelled to 22nd century Earth to see the Flesh in its early stages. By doing so, he gained the information needed to block the signal to Amy's flesh avatar, terminating it just as Amy gave birth aboard Demons Run, with Kovarian present. (TV: The Almost People)

The Doctor and Rory then searched for Amy, destroying the Twelfth Cyber Legion both to acquire her location and to make a point to her captors. In anticipation of a confrontation at Demons Run, the Doctor recruited numerous allies through time and space to help him. After a month, Demons Run was infiltrated by the Doctor and his allies, who successfully retrieved both Amy and her baby, only to learn too late that the latter was a flesh avatar, Kovarian having escaped with the real Melody. In the aftermath of the battle, River Song arrived and revealed that she was Melody to the Doctor, who left to search for the baby alone, and her parents. (TV: A Good Man Goes to War)

From Melody to River
Having been returned to Earth, Amy and Rory spent the summer of 2011 waiting for the Doctor. Ultimately, he met with them, having failed to find the young Melody. Shortly after his arrival, the three were met by Mels, Amy and Rory's childhood friend who held the Doctor at gunpoint, forcing him to take her to Berlin in 1938, her intention being to kill Adolf Hitler. As a result of Mels shooting the TARDIS control console, the TARDIS flew erratically before crashing into the Reichschancellery, where Hitler was being attacked by the Teselecta, a shapeshifting vessel of the Justice Department, whose crew travelled through time to torture criminals. The TARDIS collided with the humanoid Teselecta, which stood up again after the Doctor and company disembarked and came face to face with Hitler who, in an attempt to kill his attacker, inadvertently shot Mels.

After Hitler was incapacitated by Rory, Mels, having sustained a fatal injury, regenerated into who the Doctor and his companions knew as River Song. Shortly after regenerating, River tried to kill the Doctor. After several failed attempts, she transmitted to him poison from the Judas tree through a kiss, leaving the Doctor with minutes to live. Having been recorded in history as the Doctor's murderer, River was intercepted by the Teselecta, which began to torture her before being stopped by Amy and Rory, who forced its crew into retreat. Ultimately, the Doctor died as a result of the poison but River, having been convinced by Amy, used her regeneration energy to revive him, expending all her regenerations as a result. After being left in the care of the Sisters of the Infinite Schism, River entered Luna University, following the Doctor through archaeology. (TV: Let's Kill Hitler)

Lake Silencio
After some time at Luna University, River Song received her doctorate. On that day, she was met by Madame Kovarian and two Silents, who forced her into an intelligent spacesuit. (TV: Closing Time) The suited River was submerged in Lake Silencio, Utah, where she emerged on 22 April 2011. River met the Doctor, who had arrived to meet his death was recorded in history. However, River was able to drain the suit's weapon systems, preventing it from firing on the Doctor and thus breaking a fixed point in time, causing a new reality to be created as time began to collapse. (TV: The Wedding of River Song, The Impossible Astronaut)

In the new world, which was a combination of Earth's history, the Doctor was aware of the change in the timeline and came into contact with Amy, Rory and River, all of whom were part of a group of people who perceived the change, based at Area 52. Also present were Madame Kovarian and a group of Silents, who had been captured by Amy's forces, who wore eye drives derived from Kovarian's in order to observe the Silents. However, the Silents were able to take control of these eye drives, using them to attack their captors as they broke out of captivity to ensure the Doctor's death. Whether intentionally or not, Kovarian also began to feel pain from her eye drive. Amy, holding Kovarian responsible for robbing her of her baby, left her to be killed by the eye drive.

The Doctor, realising that the change in history would ultimately destroy reality, convinced River Song to make physical contact with him in the form of a kiss, in a wedding ceremony witnessed by Amy and Rory. Looking into the Doctor's eye, River saw that he was actually the Teselecta, with the real Doctor inside. Because she and the Doctor were the opposite poles of the disruption in time, their touching caused time to be returned to its original state, where River "killed" the Doctor. (TV: The Wedding of River Song)

Resolution
300 years into the Siege of Trenzalore, the Eleventh Doctor discussed the Silence's attempts to kill him with Mother Superious Tasha Lem, who disavowed the Kovarian Chapter. Tasha noted that, by destroying the TARDIS, they have created the very crack in the universe through which the Time Lords were calling. The Doctor observed that the Kovarian Chapter had fallen into a destiny trap; they were not able to change history because they were a part of it. He also acknowledged that he would have never lived to come to Trenzalore if not for River Song, who the Kovarian Chapter had intended to kill him. Ultimately, the siege ended without the Doctor saying his name. Instead, Clara Oswald convinced the Time Lords to assist the Doctor, who was on the brink of dying of old age with no remaining regenerations, which they did so by providing him with regeneration energy, which he used to destroy the Dalek forces assembled over Trenzalore whilst the Time Lords, electing not to return to the universe at that point, closed the crack. (TV: The Time of the Doctor) Eventually, the Time Lords returned Gallifrey to the universe more discretely, at the end of the universe. (TV: Hell Bent)