Beyond Good & Evil is an action-adventure game with elements of puzzle-solving and stealth-based games. The player controls the protagonist, Jade, from a third-person perspective. Jade can run, move stealthily, jump over obstacles and pits, climb ladders, push or bash doors and objects, and flatten herself against walls. As Jade, the player investigates a number of installations in search of the truth about a war with an alien threat.

Jade and Pey'j are care-taking the children of Hillys orphaned by the DomZ. When Jade runs out of money to run the shield that protects them, she finds a photography job, cataloguing all the species on Hillys for a science museum. She is recruited by the IRIS Network, which suspects that the Alpha Sections are behind planet-wide disappearances. Jade's first target of investigation is an Alpha Sections factory.