Mon Mothma contacted Katarn and Ors to investigate an Imperial Remnant base on Kejim after the New Republic intercepted a suspicious transmission coming from the base containing keywords such as 'Reborn' and ' Valley of the Jedi.' After infiltrating the base and fighting off Remnant forces, Katarn and Ors discovered that the Remnant was conducting experiments on crystals capable of storing the power of the Force. Kyle Katarn and Jan Ors are preparing to begin their mission on Kejim. He now works as a mercenary for the New Republic alongside his partner and lover, Jan Ors. Since nearly falling to the dark side, Katarn had given up his lightsaber and the Force. Like its predecessors, the game has Kyle Katarn as the protagonist.
The game takes place in 12 ABY, two years after the end of Star Wars: Jedi Knight: Mysteries of the Sith.