In the future, on the planet Hillys, the population suffers from constant attacks from the alien DomZ. The situation is gradually getting worse, as the rate of DomZ kidnapings increase. The Alpha Section forces, who are in charge of protecting citizens, seem to be completely ineffective, not even fighting the DomZ. In the midst of this situation, the secretive organization IRIS alleges that the Alpha Section is involved in a massive government conspiracy, and seeks to expose the truth through journalism.

You control the young reporter/photographer Jade, with her companions Pey'j and Double H. After experiencing first-hand a DomZ attack, she is contacted by IRIS, who recruit her as an action reporter. Jade is now tasked with infiltrating the Alpha Section, exposing the government conspiracy, and ultimately finding the truth for herself.

Beyond Good & Evil is an action-adventure game with diverse game play. Most of the game is based on stealth and puzzles, but there are sequences of racing, shooting, combat, and Plattform: action. There are several mini-games and even an online ranking system (used by entering codes online after they are assigned in-game when the game is saved). As the game progresses, a large story unfolds, even dealing with some social issues on the way.