The attraction contains many flying ships that help you get across the level, some of the ships contain switches that will cause them rise or sink, allowing access to new areas of the level. At the end of Level 5, Dr. Robotnik decides to take matters into his own hands.
At the start of the battle, Dr. Robotnik rises out of the sea in a machine that's surrounded by some sort of protective shield. The evil Doctor then tries to crush the player whilst still protected by the shield. Robotnik will then remove the shield, revealing the machine's true appearance. The machine will then move up and down with the remains of the shield orbiting, dealing damage if the player accidentally hits it instead. The battle ends once the Dark Ring powering the machine disintegrates, leaving Robotnik no other choice but to escape in his jet pack.
Despite its name, and use of ships, Marina Madness contains no underwater sections in gameplay.