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 increases. 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.

The player controls a young reporter and photographer named Jade with her companions Pey'j and Double H. After experiencing first-hand a DomZ attack, she is contacted by IRIS, who recruits 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 game with diverse gameplay. Much of the game is based on stealth and puzzles, but there are sequences of racing, shooting, combat, and platform action. Jade fights with her staff and also uses various abilities to execute long-ranged attacks and solve puzzles. Many of the puzzles require switching between the characters and using their special abilities; often it is necessary to coordinate the actions of two characters to achieve precise co-operation that leads to a puzzle's solution. Besides hostile areas with puzzles and enemies, there is also a city and other friendly areas to explore, where various items and gadgets can (and sometimes must) be bought. 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).