The player can choose between four nationalities: American, British, Japanese, and German. The choice of nationality affects the available ship types and characteristics of the ship parts which become available to the player throughout the game. The player can also choose to play the Normal mode or the World War II mode. In the World War II mode, technologies available will be mostly consistent with what was available to World War II-era warships. In the Normal mode, more advanced technology is available, including science fiction weapons like lasers and wave guns.
At the beginning of the game, the player is given command of a generic destroyer. As missions are completed, the player earns points and money. The points go toward crew promotions, while the money can be used to purchase ship parts from boat hulls to weapons, armor, and equipment. The money earned can also be used to develop technology in five areas: aircraft, weapons, metallurgy, engines, and electronics. The higher level of money invested in each category makes available more advanced designs.
There are five main categories of ships in this game, along letter-pair identifiers: destroyer (DD), cruiser (CL for Light/CA for Heavy), battleship (BB), aircraft carrier (CV), and battlecarrier (BC). With enough money, players can purchase a pre-built design or design their own. Pre-built vehicles also may feature parts that cannot be found in the game, so players may purchase pre-built vehicles and then scrap them for parts.
The game progresses through 40 missions through 4 theaters of 10 missions each. The first theater is set around the Mediterranean Sea and the Atlantic Ocean. The second theater is in the Pacific Ocean, the third is in the Indian Ocean, while the fourth is worldwide. Toward the end of each of these theaters is a "boss" level, in which players must sink a "supership".
A heavy emphasis of this game is the ability to customize the ships. Larger guns, faster engines, and greater anti-aircraft capability are all available to existing ships.
There are also two sequel games called Naval Ops: Commander which offers pretty much of the same gameplay, however the battle scenes are fought out in a top down view which makes things a little easier, and a later sequel, Naval Ops: Warship Gunner 2, which returned to Warship Gunner's style of gameplay, but with a new story.
A running gag in the game is that the bosses are called superships despite many of them not actually being ships.