I'm thinking it will be something like this....
There is a hugh battle with the current Emperor that finally defeats him and somehow caused you to have to be put on ice, maybe you where infected with something they could not deal with at the time so your frozen. in the mean time things heat up between the rep's and the Imp's. the Sith being sith finally fragment with each Sith lord taking what they can to forge their own little empire and what we are seeing is an unknown as of yet Sith whom has created his own empire left in the void from where the current Emperor and Sith empire came from and waging war on whats left of the Galactic Rep. and the Fractured Sith empire.