The Galactic Empire vs The New Sith Empire
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Instead of fighting the Republic, Darth Sidious' Galactic Empire is transplanted into the time of TOR and there is a war between his Empire and Lord Vitiates. For clarification, Sidious gets the half of the galaxy that the Republic has in SWTOR as well as any contested world in the game (any world that he possesses in his own time that Vitiate does not in the TOR-era).
This is both Empires at their full-power. The GE has all its forces as well as Darth Vader and the Death Star and any thing else it possessed at the time if RotJ, excepting the Galaxy Gun and the Suncrusher if it turns out that they existed at that time. The SE has all of its forces including the Sith Order, the Mandalorians and Imperial Intelligences. It also has the forces that it held at any point in the game including the superweapons from the Knight storyline and the Dreadmasters, except for the Foundry.
These terms are subject to change.