The story of Code Age Commanders is set in Dyson Sphere; a hollow world with people living on the inside. The middle of the sphere is home to the "Central Code." Every ten thousand years, the Central Code goes through a transformation, which results in the total destruction of the Dyson Sphere, followed by its rebirth. Of course, this outcome is less than desirable to the people living within the Dyson Sphere. Thus, they tried to escape by creating a gigantic station around the Central Code itself. As things usually do, things went somewhat amiss, and the station finds itself sunken to the surface along with its passengers.

Jean, one of the passengers of the station, fills the main character role in Code Age Commanders. Dropped into a world which he no longer recognizes, he sets off to find his sister Alize, another passenger from the station. Alize had been with him when the station "sank," but was soon kidnapped by a strange creature.

Thanks to the Central Code's impending transformation, the world has found itself heavily populated by strange and warped creatures. One species, called "Othelos," seek out and possess humans, turning them into what are called the "Coded." Completely stripped of free will, Coded humans become nothing more than extensions of a hive mind. On rare occasions however, humans won't turn into Coded, and instead mutate into "Warheads," who are Half-way between human and Coded and can still act on their own free will. Warheads have bodies that have evolved to the extreme, and certain actions lead to permanent abilities.

Jean finds himself becoming a Warhead, and gets caught in the middle of an Othello battle soon after setting out in search of his sister. At first glance, his body doesn't seem that much different from ordinary humans, but when a battle occurs his whole arm transforms into a weapon. As Jean levels up, this weapon levels up with him, becoming better and more versatile.

It seems as if it doesn't take long before Jean gains a few allies, but no details concerning other playable characters have been released as of yet. The battle system is also shrouded in mystery, with the only thing being known is that it will employ a "Ring Gauge System," which looks to involve a ring gauge that appears around the character. Furthermore, there will be differences between night and day in the game, though more details concerning this is also unknown.