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The Siege of Atropos was the final battle of the Founding Conflict, which closed off the Dark Times as the Time Lords defeated the last forces resisting against their binding of time.
History
Prelude
The Time Lords sought to impose their control on time to end the Dark Times. (TV: Once, Upon Time) Upon completing the Hand of Omega, Omega had declared to Rassilon and the Other that their people could use it to become the Lords of Time and impose their own order upon time. (PROSE: Remembrance of the Daleks) Rassilon ultimately decided to make the universe rational. (PROSE: So Vile a Sin)
Led by Rassilon, the Time Lords created the Web of Time, (AUDIO: Neverland) otherwise known as Spiral Politic. (PROSE: The Book of the War) Control of time was achieved by binding it to the artifical planet Time, converging in the Temple of Atropos where "all of time" would pass through six Mouri, whose wills would keep it controlled. (TV: War of the Sontarans, Once, Upon Time) The Eye of Harmony on Gallifrey acted as the "hitching post" for the structure of time Rassilon had created. (AUDIO: Neverland) The Book of the War recorded this event as the Anchoring of the thread. (PROSE: The Book of the War)
The Time Lords' control of time was deemed heresy by two Ravagers, Swarm and Azure, (TV: Once, Upon Time) who worshipped the entity that personified Time. (TV: The Vanquishers) They engaged in the Founding Conflict to overturn the order the Time Lords had wrought, believing this as an expression of a fundamental battle between space and time. (TV: Once, Upon Time) Swarm battled the Doctor numerous times, in lives that would later be erased from her memory by the Division. (TV: The Halloween Apocalypse)
The Ravagers eventually discovered the Temple of Atropos on the planet of Time. They took millions of hostages within Passenger forms and then usurped the Temple, banishing the Mouri within and allowing time to run wild. (TV: Once, Upon Time)
The Siege
On the promise of this being her final mission, the Fugitive Doctor was sent by the Division to restore the Temple and capture Swarm and Azure. She was accompanied by Karvanista and two other Division agents and infiltrated the Temple, where Swarm and Azure had setup thrones and were holding millions hostage within Passenger forms. As she carried out the mission, the Doctor experienced visions of a future self, which her comrades attributed to temporal hazing due to the condition of time.
The Doctor had the Mouri secrete themselves inside one of the Passenger forms and gave them a signal to emerge whilst confronting the Ravagers herself, during which multiple Passengers of hostages were erased by the Ravagers. The Mouri retook their positions, restoring the Temple and returning time to normal. The Doctor's allies then immobilised Swarm and Azure. (TV: Once, Upon Time)
Aftermath
Swarm was imprisoned on the Burnished Rage battleground in a containment chamber, with Division agents visiting every thousand years to check he was secure. Azure was suppressed within a human identity, Anna, and lived in Arctic Circle on Earth. (TV: The Halloween Apocalypse)
To protect them from Swarm and Azure, the Mouri were quantum locked against them. (TV: War of the Sontarans)
Legacy
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Whilst in a time storm after taking a broken Mouri's place in the Temple during the Great Disruption, the Thirteenth Doctor fell into her time stream and experienced the events of the siege from her fugitive incarnation's perspective. (TV: Once, Upon Time)