The Siege of Trenzalore, (TV: The Time of the Doctor, PROSE: Tales of Trenzalore) foretold as the fall of the Eleventh, (TV: The Wedding of River Song) was a conflict initiated by a message broadcast through time and space that no one could understand. It lasted 900 years, (PROSE: Tales of Trenzalore) coming to an end in the 50th century. (PROSE: A Perfect Christmas)
Towards the end of his farewell tour, the Eleventh Doctor wished to know the Silence's motive for engineering what appeared to be his fixed death at Lake Silencio. His search led him to Dorium Maldovar, whose severed, still living head he found at the Order of the Headless' Seventh Transept. Explaining to the Doctor that the Silence wished to avert his "dangerous" future, Dorium elaborated by telling him the prophecy, "On the fields of Trenzalore, at the fall of the Eleventh, when no living creature can speak falsely, or fail to answer, a question will be asked. A question that must never, ever be answered." Revisiting Dorium after escaping his death, the Doctor was reminded by Dorium that the future told in the prophecy was still waiting for him. (TV: The Wedding of River Song)
The Papal Mainframe arrived at Trenzalore first and, recognising the significance of the message, created a force field around the planet to protect the small village there. Unknown to them, the Weeping Angels had already arrived and hid in the snow on the planet's surface. By the time the Eleventh Doctor arrived, hundreds of ships had gathered, including flying saucers of the New Dalek Paradigm, Cyber-ships, Sontaran flagships and scout ships, Judoon rockets, Silurian Arks, and ships belonging to the Terileptils, Slitheen, Ice Warriors, Shakri, (TV: The Time of the Doctor) Krynoids, (PROSE: An Apple a Day...) and the Mara. (PROSE: The Dreaming) The Doctor later theorised that the Nestene Consciousness also seized a ship from one of the orbiting species. (PROSE: Strangers in the Outland) Mother Superious, Tasha Lem, assisted the Doctor and Clara Oswald in reaching the planet.
When the broadcast was revealed to be the Question, sent from Gallifrey, trapped in a pocket universe and emanating through a crack in time and space, 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 wouldn't bring the Time Lords back through the crack, fearing the Last Great Time War would start anew. Tasha Lem, changing the faith of the Papal Mainframe into the Church of Silence (to prevent the Doctor saying his name, bringing the Time Lords back and restarting the Time War), initiated the Siege of Trenzalore. (TV: The Time of the Doctor)
Attempts to beach the force field
Over the next three centuries, each of the Doctor's enemies tried various means of penetrating the force field created by the Church of Silence, each time defeated by the Doctor's ingenuity. It was during this time that the Kovarian Chapter led by Madame Kovarian broke away from the Church, travelled back along the Eleventh Doctor's time stream and attempted to kill the Doctor so he would never reach Trenzalore. Their first attempt involved them blowing up the TARDIS which the Doctor prevented. However, in doing this, Kovarian and her faction ended up creating the cracks in time in the first place, effectively causing what they sought to prevent. The Doctor called this the Destiny Trap: "You can't change history if you're part of it."
The fleets above Trenzalore made various attempts to sneak past the force field - such as the Sontarans using an invisibility cloak and the Cybermen using a low-tech wooden unit. (TV: The Time of the Doctor) This also incuded the Ice Warriors burying Christmas through an avalanche, (PROSE: Let it Snow) a blind Tsunami Snake, (PROSE: The Dreaming) a Krynoid. (PROSE: An Apple a Day...) and the Nestene Consciousness parachuting in Autons. (PROSE: Strangers in the Outland)
The Kovarian Chapter’s war against the Doctor
- Main article: War against the Doctor
The Kovarian Chapter of the Church broke away from the Silence and embarked on a campaign to prevent the Doctor ever arriving on Trenzalore in the first place. They arranged the destruction of his TARDIS, (TV: The Time of the Doctor) which triggered Total Event Collapse. The younger Doctor was able to avert the destruction of the universe, (TV: The Big Bang) though “scar tissue” was left behind, resulting in the crack at Trenzalore in the first place.
The Kovarian Chapter’s next attempt involved the creation of an assassin. (TV: The Time of the Doctor) They kidnapped the Doctor’s companion Amy Pond who was pregnant with a child conceived during flight through the Time Vortex and replaced her with a Flesh duplicate to prevent the Doctor discovering their act. Amy was held at Demons Run, TV: A Good Man Goes to War) and was finally awakened on the verge of giving birth, when the Doctor had discovered the ruse. (TV: The Almost People) After she gave birth to a child, Melody Pond, the Silence made preparations to defend Demons Run from the Doctor , enlisting an army of clerics led by Colonel Manton and allying with the Order of the Headless. In the ensuing Battle of Demons Run, the Doctor and his allies took the facility however Kovarian escaped with baby Melody by placing a Flesh duplicate with her mother. (TV: A Good Man Goes to War) The clerics and Headless Monks abandoned Kovarian after the loss of Demons Run. (AUDIO: The Furies)
Kovarian initially raised Melody at Concorde Dawn, (AUDIO: The Furies), however she was eventually taken to Earth in 1969 where she was raised in an orphanage supervised by Silent priests. The Silents infiltrated Earth across time to manipulate the human race to produce the resources they needed, keeping Melody in a modified Apollo 11 space suit. Melody used the suit’s communications to ask for help and was put through to President Richard Nixon. Her bizarre calls attracted the attention of the Doctor, who arranged the overthrow of the Silents by conditioning humanity against them using the Apollo 11 Moon landing broadcast. Melody escaped her captors, eventually regenerating after spending months on the streets. (TV: The Impossible Astronaut, Day of the Moon)
In her new incarnation, Melody became the childhood friend of her parents, under the name Mels. Eventually catching up with the Doctor in 2011 Mels forced him to take her to Berlin in 1938 and attempted to realise her childhood programming by killing the Doctor. Her parents talked her out of it, and she sacrificed her remaining regenerations to save him instead, becoming River Song. (TV: Let’s Kill Hitler) Despite River rejecting her programming, Kovarian arranged for her to be forced to assassinate the Doctor at Lake Silencio as part of a fixed point in time it was believed the Doctor could not escape. Unaware he had made arrangements to survive by being inside the Tescelecta, River attempted to defy the fixed point resulting in the breakdown of history. In the ensuing alternate timeline, Kovarian and the Silents attempted to kill the Doctor themselves, but were defeated and killed by Amy and Rory of this timeline. The Doctor revealed his ruse to River and married her, compelling her to complete the fixed point and restore history to normal. (TV: The Wedding of River Song)
Still alive in the normal history, (TV: The Wedding of River Song) Kovarian eventually learnt of the Doctor’s survival and attempted to use Proto-Time Lords created from River’s DNA to assassinate the Fifth Doctor, with Brooke's first incarnation succeeding. (AUDIO: My Dinner With Andrew) River managed to turn her siblings against Kovarian, with Brooke's second incarnation choosing to alter history to undo her assassination of the Doctor. Kovarian was held captive by the Proto-Time Lords, with River ignoring her pleas for mercy. (AUDIO: The Furies)
Fall of the Mainframe
Three hundred years into the Siege the Daleks turned their attention to the Church itself. After calling for reinforcements on a daily basis, they assaulted the Mainframe, turned everyone into Dalek puppets and penetrated the field afterwards, followed by the Cybermen and the other fleets. (TV: The Time of the Doctor)
End of the Siege
750 years into the Siege, the Mara entered Christmas and possessed the town's children, trying to force the Doctor to say his name and begin a new Time War, but the Doctor defeated them. (PROSE: The Dreaming)
Allying himself with the Papal Mainframe's soldiers and Confessional Priests (now known as the Silents), the Doctor repelled each attack, and eventually all attackers had either been destroyed or had retreated save for the Daleks who continued to attack the village in Dalek Attack Ships (TV: The Time of the Doctor) and the Parliament of the Daleks. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) Finally, dying of old age after nine hundred years of fighting, the Doctor was ready to admit defeat to his oldest enemies. However, when the Time Lords used the crack to grant him a new regeneration cycle, having been persuaded to do so by Clara Oswald, the Doctor was quick to defy the Daleks, and used the excess energy from his thirteenth regeneration to destroy their forces, effectively ending the siege (TV: The Time of the Doctor) and changing the future he had previously been made aware of. (TV: The Name of the Doctor)
With the Daleks defeated, the people of Christmas saved and the crack finally closed by the Time Lords, the Doctor retreated to his TARDIS. Despite being restored to a youthful appearance during his regenerative "reset" on the clock tower, he was still dying of severe old age. Before regenerating, he used the TARDIS telephone to send a parting message to Clara in the near future relative to his regeneration, as a way of easing the stressful experience of adjusting to his new incarnation, then reunited with the present-day Clara. (TV: The Time of the Doctor, Deep Breath)
The Siege of Trenzalore was considered by some to be the true end to the Time War. (PROSE: The Secret Lives of Monsters) Tasha Lem died during the Siege. She was the last Mother Superious of the Papal Mainframe. She was buried in a tomb of ice, which took thirty years to carve, with a TARDIS key as a sign of respect for all she had done. (PROSE: A Perfect Christmas)
Freed from his obligations to both the Time Lords and the people of Christmas, the Doctor set the TARDIS in flight and made good his departure from Trenzalore. After saying an emotional farewell to his companion, he finally succumbed to his advanced age and regenerated into the Twelfth Doctor. (TV: The Time of the Doctor)
The siege also confirmed to the Time Lords they had found their home universe to return to, though, when Gallifrey returned, they placed their home at the end of the universe in order to stay safe. (PROSE: A Brief History of Time Lords)
Historians who studied the history of the Dalek race believed that the New Dalek Paradigm had committed the entirety of its military might to the Siege and thus, the Dalek race had finally been destroyed at the Siege's end, though, given the many other final defeats of the Daleks, they had reason to doubt their theory. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)
In an alternate timeline, the Time Lords never gave the Doctor a new regeneration cycle, and the Siege of Trenzalore ended in a victory for the Doctor's enemies with the Doctor himself dying. Trenzalore became a desolate, volcanic wasteland with its moons and rings destroyed and a battlefield graveyard covering the planet's surface for the millions who had died during the battle. The biggest of these graves was the Doctor's in the form of his dying TARDIS, which was suffering from what the Doctor called a "size leak".
According to the Great Intelligence, while, to most involved, the Siege was a massive battle that millions died in, to the Doctor, it was a "minor skirmish" compared to the other bloody battles he had fought in, particularly during the Last Great Time War. (TV: The Name of the Doctor)