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The Second War in Heaven is the most specific name available for the conflict usually referred to by its participants as simply The War (EDA: Interference, FP: The Book of the War).
The first War in Heaven was considered to have been the hostilities between the Time Lords and the Great Vampires/Yssgaroth (FP: The Book of the War). From the comfort of victory, Gallifrey came to regard the intervening Time Wars fought in the generation after Rassilon's (NA: Sky Pirates!, PDA: The Infinity Doctors) as simply their 'tweaking' of the universe (FP: The Cosmology of the Spiral Politic) and so those campaigns escaped such grandiose appelation.
This particular Time War was fought, or would have been fought, between the Time Lords and a hostile process of history they referred to as The Enemy.
It should not be confused with the Last Great Time War between the Time Lords and the Daleks.
The Laws of Time weakened during the conflict's prosecution, allowing events from the War-era to interact with those from before its outbreak. Ironically, this ultimately lead to the War itself being averted by the pre-emptive destruction of Gallifrey. The destruction may have proved temporary on this occasion (EDA: The Gallifrey Chronicles), but the war was forestalled.
Despite this, many events that would have taken place during the War are well documented and likely continue to hold consequences for some. For example, the Osirian Court's timeline moves in the opposite direction to Gallifrey's so events already in their past occured as part of this averted future war. Likewise, the City of the Saved is immune to any depletionary alterations to history, so the removal of the War from the rest of the continuum would not have slowed its progress there.
Cracks in Time
The Laws of Time traditionally prevent Gallifrey's present from interacting with its past or future (NA: Lungbarrow). Such was the temporal chaos of the War however, that combatants from the War-Era and Time Lords from the pre-War-Era encountered each other on a number of occasions.
The Doctor found himself participating in an auction for his own corpse alongside various Wartime factions who wished to weaponise it (EDA: Alien Bodies) and agents of The Order of the Weal encountered War-era agents of Faction Paradox before House Paradox had even abandoned Gallifrey (FP: The Book of the War).
Knowing that the War was approaching, Lady President Romana began stockpiling weapons in The Slaughterhouse, an arsenal protected by a time eddy. Even at this early stage, Romana had become War Queen and Mistress of the Nine Gallifreys (EDA: The Ancestor Cell).
Romana was also aware that new TARDISes would be required for the war and so despatched two of her most trusted agents, Gandar and Cavis, to capture the newly formed Type 102 TARDIS known as Compassion from the Eighth Doctor (EDA: The Shadows of Avalon).
Ironiclly, all this foreknowledge of the War eventually resulted in its own aversion via Gallifrey's pre-emptive destruction (EDA: The Ancestor Cell).
It would seem that Gallifrey would eventually be restored in order to be destroyed a second time in the Last Great Time War (EDA: The Gallifrey Chronicles). Nevertheless, its destruction on this particular occasion appears to have prevented this particular war. What follows is an account of how events progressed before this paradox removed them from the timeline.
Detail to be added
The War Begins
The first battle began on Dronid as the Time Lords realised the true magnitude of the threat they were facing on discovering the Enemy possessed their own Web of Time. (FP: The Book of the War).
Detail to be added
Future History of The War
It is indicated that the Time Lords were not winning The War. There were at least nine clones of Gallifrey. War Looms clogged the atmosphere of at least on of the Gallifreys with biodata soot. (EDA: The Taking of Planet 5)
Preemptive Strikes
The Time Lords attempted to beat The Enemy by taking a preemptive strike at The Enemy's home world, but not via conventional time travel. The Time Lords set a giant Gallifreyan warship containing The Cold and aimed it at what they believed to be The Enemy's home world: Earth. (EDA: Interference)
Participants
Although the conflict was primarily between the Time Lords and the Enemy, other power blocs became heavily involved as they sought to either evade or exploit the War.
Faction Paradox's stance proved the most opportunistic and changable. At times they over ambitiously launched direct attacks on the Time Lords (FP: The Book of the War), at times attempted more subtle subversion of their activities (EDA: Interference) and eventually found themselves negotiating to be reinstated as a House of Gallifrey (BBV: 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 (FP: The Book of the War).
Various Posthuman groups allied themselves with The Enemy (FP: The Book of 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.(FP: The Book of the War).
Amid the chaos, Gallifrey found time to attack the Osirian Court. Threatening to flood a crucial point in history with vampires, Sutekh effectively blackmailed the Time Lords into a peace treaty (FP: Coming to Dust). Perhaps this was similar to the non-aggression pact between Gallifrey and The People (NA: The Also People), which appeared to endure into the War-era (BNA: Dead Romance), sparing the universe the ruinous effects that would of resulted from them entering the fray as time-active combatants (BNA: Walking to Babylon).
It has been suggested that the War itself was allowed to escalate out of all proportion and that the real threat to Gallifrey came from within (FP: Warlords of Utopia). Indeed, the Houses of Gallifey were not above in-fighting, especially the ruling six; Mirraflex, Xianthellipse, Arpexia, Dvora, Tracolix and Lineacrux (FP: The Book of the War). It was House Lolita though which most ruthlessly persued its own interests (BBV: The Shadow Play, In the Year of the Cat).
Technology and Development
Time Lords from a later period in 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 utilized by Time Lords on missions. (EDA: Alien Bodies, The Taking of Planet 5)