"Nautilus" starts with player one in control of the submarine, visible in the lower pane of the split-screen display. The joystick allows the player to move left and right or rise and sink. The player can shoot their Thunderbolt torpedoes to the right or left in the direction of travel. The primary task for the player is to move into location beside the various underwater buildings and destroy them with their torpedoes in order to expose their energy core, which can be picked up by moving over it. The player wins the level by collecting all of the cores.