Alter A.I.L.A. Genesis takes place in a post-apocalyptic world. You play the role of a young man known as Leon, who seeks to survive in the harsh environment he is brought into.

Exploration is done mainly via a side-scrolling view. In certain areas, an exclamation mark will sometimes appear, indicating the presence of hostiles. Press Z when this happens to initiate battle, or wait to let it pass. Sometimes battle will be unavoidable. When walking, enemy encounters won't occur.

The battle system revolves mainly around each character's Abilities, which are a set of commands specific to that character. Abilities require AP and EX to use. AP is gained every time a character takes a turn.