The game is a one-player simulation of naval combat, in which the player commands an individual ship. In the opening cutscene, a World War II-era destroyer similar to its predecessor, Naval Ops: Warship Gunner. The game uses the same type of warships and most technologies alloted in Warship Gunner.
The game differs from both Warship Gunner games, by having look-down view of playing instead of third-person view. You are also alloted escort/support vessels to assist you in missions. You can also re-arrange these escorts to different formations to allow better use of their abilities. The games still allows the customization of your "flagship" or "command ship" as in Warship Gunner(s) games.
Weapon systems are the same, but you'll note that power and effectiveness of these weapons will differ from other Warship Gunner games. You may find them not as powerful, or as effective in some cases.
Story wise, in first Warship Gunner, the player's ship is one drawn from another world. Namely World War II of Earth. In Commander, the roles are reversed, the player is now the native of the alternated world. The player witnessing people and technology coming from another world. However, not necessary from our Earth.
There are many hulls available to the player including drillships and double hull ships. However some hulls can only be used by getting a certain score on a certain level such as getting a drillship for beating the "Arahabaki2". Only type real naval vessel is not available to the player is the submarine. Naval Ops: Warship Gunner 2, the other sequel to Naval Ops: Warship Gunner, allows use of player controlled submarines.