The story of Sub Rebellion takes place 15 years after a catastrophic event that causes earthquakes, destroying most human civilization. The remnants of humanity live in the depths of the oceans, where an evil military-industrial complex seeks total control.
The player controls the Chronos, the Alliance's newest sub, on a mission to defend humanity from this foe. The game begins with the maiden voyage and takes the player through various missions, including sea-level fighting and boss battles. The submarine has complex controls, allowing it to rapidly ascend or descend, which are essential in combat.
The Chronos is equipped with various weapons and equipment, such as cannons, torpedoes, and special weapons. These can be upgraded throughout the game by completing missions and collecting artifacts. With its advanced features, the player must navigate through treacherous underwater environments to emerge victorious.