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The Corporeal PlaneEdit
The war emerged during the Dominion War when the Founders ordered a small fleet to go through the newly formed wormhole in order to determine if it connected to the Gamma Quadrant so they could use it to summon reinforcements for their war against the Federation. Several Cardassian and Jem'Hadar ships were sent under the supervision of Weyoun with only the Vorta returning at the head of Grigari fleet.
Weyoun's passage through the anomaly had changed him and he became the True Emissary of the True Prophets thus beginning a war against the other powers, including his former masters, and became the leader of the Bajoran Ascendancy. The entire Cardassian Union and its territories were wiped out along with all Dominion presence.
The newly formed Bajoran Ascendancy would fortify its strongholds and begin attracting worlds that were awaiting entry into the Federation. This would be the start of a new war as the Ascendants would sabotage Federation worlds which destroyed the command as well as control base of Starfleet causing it to weaken while the Grigari served as a potent weapon against Bajors enemies. During trade negotiations at Sector 001, the Grigari 'mistook' a Federation sensor barrage as an attack and destroyed Earth. The Klingons were defeated by a Grigari fleet during their implementation of Project Looking Glass and the Grigari spread a Nanospore virus to numerous Human colonies through transporter mechanisms which nearly brought about the extinction of both species.
The Romulan Star Empire was content to its enemies crushed and formed an alliance with the Ascendancy only to find sabotage as well as assassinations of their leaders. Where the Federation and Klingons were being destroyed from the outside, the Romulans were being weakened from within. The scattered remnants of Starfleet abandoned the Prime Directive and the Temporal Prime Directive in order to accomplish, by any means, the destruction of the Ascendancy power base on Bajor which was heavily fortified.
While the war was seen by many as a struggle between two powerful nations, the truth of the matter to the Bajoran people was it was a struggle between the True Prophets and the False Prophets. The goal of the fighting between the Ascendancy and the remnants of Starfleet was to await the prophecised time of the Day of Ascendancy when the False Emissary would return at the time when the two temples would open in conjunction with one another and merge to become the One True Temple.
The resulting action would have produced a powerful subspace shockwave that would have destroyed the universe though the Ascendant followers believed that this act would make them one with their gods.
The entire timeline and war was erased when Captain Benjamin Sisko managed to return to his time period and prevented the Red Orbs of Jalbador forming the wormhole. (DS9 - Millennium novels: The War of the Prophets, Inferno)