Kyle Katarn returns from Star Wars: Dark Forces as the protagonist. His plans are, however, stopped by Kyle Katarn, who arrives and kills him in a lightsaber duel. At the valley, Jerec plans to absorb the ancient power that lies in the valley. During the game Katarn encounters the Dark Jedi and finds the map to the Valley of the Jedi on the planet Ruusan. Katarn receives help from his trusted partner and pilot, Jan Ors. He is granted a lightsaber and a quest to protect the Valley of the Jedi by a hologram of his father contained in the disc. After retrieving the disc, Kyle returns home to the planet Sulon where he is able to read the disc with his droid WeeGee. Meanwhile, the mercenary Kyle Katarn chases the informant droid 8t88 for a data disc that belonged to his father, Morgan Katarn.
The Dark Jedi Jerec and his six Dark Jedi seek the map to the Valley of the Jedi and captures the Jedi Qu Rahn for it.
Star Wars: Jedi Knight: Dark Forces II takes place a year after the second Death Star has been destroyed.