Siege of Trenzalore

The Siege of Trenzalore was a conflict which lasted 900 years, (PROSE: Tales of Trenzalore: The Eleventh Doctor's Last Stand) initiated by a message broadcast through time and space that no one could understand.

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, the Weeping Angels had already arrived and hid in the snow planetside. By the time the Eleventh 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. Mother Superious, Tasha Lem, assisted the Doctor and Clara Oswald in 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. 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 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, but the Doctor defeated them. (PROSE: The Dreaming)

The Daleks, however, 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. However, when he was unexpectedly granted a new regeneration cycle by the Time Lords through the crack in time at the demand of Clara Oswald, he was quick to defy the Daleks, and used the excess energy from his 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 )

Aftermath
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 newly regenerated self, then reunited with the present-day Clara. (TV: The Time of the Doctor, Deep Breath) After saying an emotional farewell to Clara Oswald, he finally succumbed to his advanced age and regenerated into the Twelfth Doctor. (TV: The Time of the Doctor)

Alternate timeline
In an alternate timeline, the Siege of Trenzalore ended in a victory for the Doctor's enemies with the Doctor himself dying. Trenzalore became a desolate wasteland with its moons and rings destroyed and a battlefield graveyard for the millions who had died during the battle left on the planet. The biggest of these graves was the Doctor's in the form of his dying TARDIS. (TV: The Name of the Doctor)