War in Heaven

The War was a temporal conflict between the Great Houses and their enemy. Several other parties became involved in a shifting configuration of alliances, notably including Faction Paradox, the Remote, the Celestis, and posthumanity. Because the Protocols of Linearity were worn down, it was difficult or impossible to determine a "final" outcome. (PROSE: The Book of the War)

Before the War
The Homeworld existed in cultural stasis for millions of years before irregularities in the breeding engines caused four "mutations". One of these was the Imperator, (PROSE: The Book of the War) who foresaw that the Great Houses were heading for conflict and attempted to prepare by giving the Homeworld a more active role in the Spiral Politic. (PROSE: The Return of the King, The Book of the War)

Greyjan the Sane also foresaw the War and made plans for the Nine Gallifreys to be created through crypto-forming as a precaution. This plan was eventually implemented by Romana III, who became War Queen on one Gallifrey and began stockpiling weapons in the Slaughterhouse. (PROSE: The Ancestor Cell)

Romana planned to use Bull-TARDISes to mate with Compassion to create a new Type 103 TARDIS. (PROSE: The Shadows of Avalon) Though this plan failed, (PROSE: The Ancestor Cell) the War King eventually negotiated the creation with Compassion to create 103-form timeships for the War.

The Great Houses first learned of the War when the War King returned to the Homeworld with knowledge of the Enemy. He was appointed as Lord President of the Great Houses. (PROSE: The Book of the War)

Beginning of the War
On Dronid, tensions between agents of the enemy and the Great Houses gradually escalated until a member of the Great Houses went there to try to find an agreement with an enemy contact. This member of the Great Houses was killed, and the first battle of the War began. (PROSE: Alien Bodies, The Book of the War)

Immediately, the enemy and the Great Houses attacked each other at many points of space-time. The enemy attempted a direct attack against the Homeworld itself, which destroyed many Homeworld technologies. (PROSE: The Book of the War)

The Doctor found himself participating in an auction for his own corpse against Wartime factions who wished to weaponise it. (PROSE: Alien Bodies)

War looms clogged the atmosphere of at least one of the Gallifreys with a biodata soot. These looms produced soldiers all day and night to provide the Time Lords with fodder for the War. (PROSE: The Taking of Planet 5)

The Time Lords attempted to beat the enemy with a preemptive strike at their homeworld, which they believed to be Earth. Instead of using conventional time travel, they built a giant warship containing the Cold and sent it to Earth. (PROSE: Interference)

Amid the chaos, the Homeworld found time to attack the Osirian Court. Threatening to flood a crucial point in history with vampires, Sutekh effectively blackmailed the Great Houses into a peace treaty. (AUDIO: Coming to Dust)

Participants
It was suggested that the War was allowed to escalate out of all proportion and the real threat to Gallifrey came from within. (PROSE: Warlords of Utopia) Indeed, the Houses of Gallifey were not above in-fighting, especially the ruling six: Mirraflex, Xianthellipse, Arpexia, Dvora, Tracolix and Lineacrux. (PROSE: The Book of the War) It was House Lolita, though, which most ruthlessly pursued its own interests. (AUDIO: The Shadow Play, In the Year of the Cat)

Although the conflict was primarily between the Time Lords and the Enemy, other powers became heavily involved as they sought to either evade or exploit the War.

Faction Paradox's stance proved the most opportunistic and changeable. At times they over-ambitiously launched direct attacks on the Time Lords (PROSE: The Book of the War), at times attempted more subtle subversion of their activities (PROSE: Interference - Book One) and eventually found themselves negotiating to be reinstated as a House of Gallifrey. (AUDIO: The Shadow Play)

The Remote were perhaps even more unpredictable; their anarchistic nature utterly committed them to the overthrow of whichever the dominant power was at any given time.

Various posthuman groups allied themselves with the Enemy.

Grandfather Halfling often left the City of the Saved to participate in the War.

From what they assumed was the safe vantage point of non-existence, the Celestis treated the War as a game, sometimes interfering on Gallifrey's behalf and sometimes supplying the Enemy with weaponry. (PROSE: The Book of the War)

Breakdown of linearity
The events leading to the end of the War began on the planet Dust. (PROSE: The Ancestor Cell) Faction Paradox came to Dust to influence I.M. Foreman's regeneration with a biodata-altering virus, but their plan took an unexpected turn when the Third Doctor and Sarah Jane Smith came to the planet. Instead of infecting I.M. Foreman, the virus was attracted to the Doctor when he was shot by a local. Shortly afterwards, the Doctor regenerated. (PROSE: Interference - Book Two)

With history changed by the Third Doctor regenerating on Dust instead of UNIT HQ, the timelines became much more uncertain and malleable. Some regions of space-time degenerated into a series of realities which formed the Obverse. (PROSE: The Ancestor Cell) A cataclysmic war began between the inhabitants of the main universe and the inhabitants of the newly formed Obverse. (PROSE: The Blue Angel)

This instability in time also affected the past of the Time Lords. Romana was made the War Queen and mistress of the Nine Gallifreys. She began stockpiling weapons in The Slaughterhouse, a secret arsenal protected by a time eddy. (PROSE: The Ancestor Cell) She planned to use Bull-TARDISes to mate with Compassion to create a new Type 103 TARDIS.

In this new history, Romana dispatched two of her most trusted agents, Gandar and Cavis, to capture Compassion while she transformed into a Type 102 TARDIS in Avalon. While the agents managed to almost start a nuclear war between humans and avalonians, they did not capture Compassion, who escaped with the Eighth Doctor and Fitz Kreiner. (PROSE: The Shadows of Avalon)

End of the War
After the Doctor installed a randomiser inside her, Compassion managed to elude the Time Lords for a considerable time, (PROSE: The Fall of Yquatine, Coldheart, The Space Age) but she was eventually found by an operative in the 19th century. (PROSE: The Banquo Legacy)

By the time Compassion was brought to Gallifrey, the planet was the epicentre between two conflicting histories; the Edifice loomed in Gallifrey's sky containing a timeline where the War never existed while an army of Faction Paradox members coming from near the end of the war attempted to invade Gallifrey. By resurrecting Greyjan the Sane, Faction Paradox took control of the planet and began merging it with the Eleven-Day Empire. The Eighth Doctor confronted Grandfather Paradox in the Edifice and restored the original timeline, at the cost of destroying Gallifrey. In the new timeline, the Doctor would never become Grandfather Paradox, would never be contaminated by the biodata-altering virus on Dust and the Enemy would never exist to threaten the universe. (PROSE: The Ancestor Cell)

Technology and development
Time Lords from a later stage of the war did not have humanoid form. Only the 'Generals' had totally humanoid forms.

Type 102 TARDISes and War TARDISes were in full use by The War. 102s were used by Time Lord agents whilst War TARDISes were utilised by Time Lords on missions. (PROSE: Alien Bodies, The Taking of Planet 5)