Controlling multiple motors the Pilot guides the submarine through the treacherous waters of the Abyss. With the help of the Radio, the Pilot avoids obstacles and the walls of the ever smaller caves and tunnels of the Abyss. During battles with monsters and rival submarines, the Pilot must communicate with the Gunner to coordinate torpedo fire with evasive maneuvers.

Additionally the Pilot must monitor fuel and oxygen levels in the submarine. He is able to replenish these resources by stopping at an oxygen pad or fuel pad respectively.