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The Siege of Trenzalore was a conflict which lasted for centuries, initiated by a message broadcast through time and space that no one could understand.
History
The beginning
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, Weeping Angels had already arrived and hidden in the snow planetside. By the time the Doctor arrived hundreds of starships had gathered, including those of the Daleks, Cybermen, Sontarans, Slitheen, Judoon, Terileptils, Silurians, Ice Warriors, Autons, Krynoids, and the Mara (possibly the Monoids, Racnoss, and Pyroviles also participated). Mother Superious Tasha Lem assisted the Doctor and Clara Oswald reaching the planet.
When the broadcast was revealed to be the First 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)
The conflict
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. (TV: The Impossible Astronaut/Day of the Moon, A Good Man Goes to War/Let's Kill Hitler, Closing Time, The Wedding of River Song) Their first attempt involved them blowing up the TARDIS which the Doctor prevented. (TV: The Pandorica Opens/The Big Bang) 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 or the Cybermen using a low-tech wooden unit.(TV: The Time of the Doctor) 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, though the Doctor defeated the Mara. (PROSE: The Dreaming) While this happened the Daleks turned their attention to the Church itself. After calling for reinforcements, they assaulted the Mainframe, turned everyone into Dalek puppets and penetrated the field afterwards, followed by the Cybermen and the other fleets. 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 Fighter Pods and a massive Dalek saucer. The Doctor, dying of old age by this time, made ready to sacrifice himself to the Daleks when he was granted a new regeneration cycle by the Time Lords through the crack in time at the demand of Clara Oswald, and used his excess regeneration energy to destroy the Dalek forces, effectively ending the siege. (TV: The Time of the Doctor)
Aftermath
With the Daleks defeated, the people of Christmas saved and the crack closed by the Time Lords, the Doctor retreated to his TARDIS. After an emotional goodbye to Clara Oswald, he finally succumbed to old age and regenerated into the Twelfth Doctor. (TV: The Time of the Doctor)
In an alternate timeline where the Time Lords never gave the Doctor more regenerations, the Doctor died on Trenzalore. This timeline was visited by the Great Intelligence and the Doctor. In this timeline Trenzalore was a cracked, ruined world, rather than the beautiful planet it was when he arrived the second time. There he saw millions of tombs and graves, the result of a battle, the largest of which was his own, comprised of his dying TARDIS. (TV: The Name of the Doctor, The Time of the Doctor)