Emperor Palpatine reigns the galaxy, along with his pupil Darth Vader. he is obsessed with destroying what remains of the Jedi, and gathers several Sith warriors to take revenge.
After the defeat at Agamar, Darth Vader discovers that both Master Yoda and Master Vaal, are training a new apprentice who is rumored to be able to defeat the sith, now he takes a personal vendetta against the rest of the Jedi order.