The game switches between two gameplay modes: an isometric open-world perspective reminiscent of the Strike series where the titular craft is sails through the depths of the ocean completing objectives, and more action-oriented side-scrolling shoot 'em up sections. The exception is the Game Boy version, which only has side-scrolling sections and a different set of missions.The player earns cash from completing objectives and missions, which can be spent to upgrade the SeaQuest DSV. The player doesn't need to spend money on repairs: the ship repairs itself automatically over time. Threats tend to include pirates and terrorists as well as natural disasters and the risk of oxygen deprivation.
