The story of El Shaddai takes place in a fantastical interpretation of biblical themes, taking primary inspiration from the apocryphal Book of Enoch. Enoch is sent by God to capture the angels which have lapsed in their duties to watch over the human world. These angels, called Grigori, became fascinated with their charges and renounced Heaven to live and breed among the humans. Enoch must traverse their realms, battle their aberrant Nephilim offspring, finally locating the fallen angels and bring them back into Heaven's fold. As Enoch journeys, he is assisted by the head archangel Lucifel.
El Shaddai is a third-person action game which emphasizes platforming and melee combat. The combat system uses very few buttons, instead relying on button timing to effect light, heavy, and counterattacks. Enoch has no weapons of his own and must rely on stealing enemies' weapons via counterattacks. These weapons degrade and must be periodically "purified" or discarded for new ones. Combat occurs periodically in arena-like encounters, which then give way to either 3D exploration or 2D platforming. The game's art style is primarily watercolor, though each angel's realm has a distinct theme.