Back Story
You play Kyle Katarn the mercenary hero from Dark Forces who successfully infiltrated the Empire. Jedi Knight: Dark Forces II continues the story of Katarn as he embarks on a quest into his past and learns the mysterious ways of the Jedi. Your father has been murdered by Jerec the most powerful of the seven Dark Jedi. Jerec wants to unlock the force energy of thousands of past Jedi Knights held in a hidden Jedi burial ground. Your father died keeping the burial ground's location a secret from Jerec. As Kyle, you must stop Jerec's evil quest and avenge the death of your father. This task forces to decide his destiny. If he chooses the dark side, he will come into enormous power. If he chooses the light side, he faces seemingly insurmountable evil. Whatever path Katarn chooses will change the face of the galaxy forever.
When Kyle initially discovers the force he is uncommitted to either side. Eventually, he develops his Force powers and must make a choice. During the game, your actions help to determine your alignment to either the dark or light side. If you choose the light side, you'll want to stop jerec from unleashing his evil on the galaxy. If you choose the dark side, you'll want to stop him and seize the power for yourself. To find the powerful burial ground, you'll need to follow scant clues left by your dead father and his allies. Along the way, you aspire to become a Jedi Knight yourself, though whether it's good or an evil Jedi is yet to be decided.
This is from the manual for the game.