Emperor shows up on Ziost, starts possessing lots of people and killing everyone else. Emperor gets stronger for everyone who dies. Your hero swoops in to save the day and works with Theron and Lana. A third spy character, somewhat minor, shows up, and is playing both Lana and Theron and secretly works for Supreme Chancellor Suresh. Your hero unwittingly lowers the planetary defenses and Suresh sends an entire Republic fleet to attack Ziost. This is bad, as we have established, more deaths = more powerful Emperor. Lana and Theron figure out that shocking possessed people makes the Emperor lose control over them, at least temporarily. There is a squad of elite Jedi that Theron brought to Ziost that (oops!) became possessed and are causing a lot of trouble. You fight the Jedi leader/Emperor, Lana/Theron shocks most of the possessed people into becoming unpossessed, and you are left with the choice to mercy kill the Jedi, have the Empire experiment on her brain to figure out how the Emperor possessed her, or send her to Tython where (hopefully, maybe) the other Jedi can repair her mind. In one final scene, the disembodied voice of the Emperor says he enjoys having you around because you entertain him, but basically there is nothing you can do and he is gonna win and he hopes you are still alive to see it all happen. Then you get a scene of all the people you just freed from his mind control being possessed yet again. So technically, the Emperor was right.
You then go to the orbital station above Ziost and when you click on the shuttle to the surface, the game basically tells you HEY THIS IS A BIG IMPORTANT PLOT PIECE AND IT'S GOING TO CHANGE SOME SHIT SO MAKE SURE YOU HAVE EVERYTHING DONE BEFORE YOU MOVE ON. So after you click it, you get a CS where the Emperor destroys all life on Ziost pretty easily. The planet turns to ash and everyone on the surface gets dusted like a vampire from the Buffy TV show. Then you can do daily quests on the ruined planet.
So basically nothing you did really matters and the Emperor is fucking shit up left and right.