Prologue:
This is a Star Wars AU in which somethings get is changed. At some point after the events of episode 9, someone from the 1st order uncovers a time machine in the unknown regions. He uses it to go back 3,600 years to warn darth Malgus that his plan to take over the Galaxy will fail and that the best course of action would be to go into exile. Malgus responds by deploying a small number of troops to the unknown regions, making plans to fake his death, and going along with his original plan. So the battle of illuminati and false emperor flashpoint happen and malgus fakes his death.
The unknown regions were rather undeveloped but there was hidden Rakata technology which allowed the malgus remnant to develop on the planets on which it was hiding. Meanwhile, emperor malgus was placed in carbon freezing until the day the empire was ready to defeat the republic once and for all. After faking his death at oricon, cipher nine, who swore loyalty to malgus, went to recruit the old imperial intelligence for the new empire.
And for the next 3,600 years, the empire remained hidden while other entities which challenged the republic rose and fell. 2,000 years into the exile, darth bane found the hidden empire. He swore to destroy it for it did not follow the rule of two and would present a great threat to any galactic rule by darth bane's order. He fought through brutal encounters with imperial troops and with lords but he made it out ok. Stories of this hidden empire were passed down from master to apprentice and eventually, these stories felt more like legends if anything.
Back in the known Galaxy, the republic was dealing with the confederacy of independent systems. Near the end of 20 BBY, darth malgus was unfrozen as the hidden empire made the the final preparations necessary to wipe out the republic and rule the galaxy and perhaps even more.
Author's Note:
This story will have many chapters which will be uploaded from once every two days to once a week. A fair warning: this story heavily incorporates Star Wars lore so if you're a newbie to Star Wars, this isn't for you though I will try to cite where the thing appears. I know that since I'm writing an AU fanfic about the Star Wars Galaxy on a whole, this creates cannon issues since, you know, Disney deleted the EU (makes me wanna beat Disney) so here's the deal: all EU which takes place during or before the clone wars is recognized unless it contradicts with the clone wars series or prequels. The exception to this will be astrographical (basically geography) lore since they aren't elaborated enough upon and the populations are often too small. Also, this fanfic will factor in realism a little more. The force is not caused by midi chlorians but rather by dark matter which was harnessed by the celestials. My fanfic has Star Wars set in the andromeda Galaxy so long ago that we see it as it was between episodes 7 and 8 (the galaxy is 2.5 million light years away which means that this takes place 2.5 million years ago).