In short, you become the Hand of Jadus, his personal assassin.
You get the same missions but with different contexts and objectives, fitting your new role as the Hand of Jadus, his personal assassin. Rather than protect/help NPC S for reason I, you're tasked to kill them for reason J.
The main context difference is your relationship to Imperial Intelligence. You're a hero if you stop Jadus, but if you side with Jadus many of them see you as a sell-out to the Sith and don't work/talk with you anymore.