The plot of Metamor Jupiter is simple: a biological mutation causes an alien race to spread all over the galaxy. Armed with advanced technology, the aliens sent their machines and robots to face humanity in a cosmic battle. To counter that, the humans draw from the newly discovered crystal energy to deploy a unit of powerful fighter crafts, which can change their shapes in an instant, adapting to every situation.
The player controls one of such crafts, and has to fly and shoot his way through side-scrolling levels populated by regular enemies, bosses, and various types of hazards. Other fighters will accompany the player-controlled machine from time to time, but they usually don't survive the robotic onslaught, and the player character is left to fend for himself.
As the premise implies, the defining feature of the game is the fighter craft's ability to change shapes. The three main variations have two weapons each, which are suited for different situations. For example, one of the forms has vertical fire, but lacks powerful explosives; another can drop bombs, but has a slow forward beam attack, etc. Each of the forms can gather power-ups, which will strengthen the conventional weapons.
Unlike most shooters of this kind, there are no "lives"; instead, the player-controlled plane has a set amount of hit points, parts of which are depleted when it gets hit. Hit points can be restored by catching power-ups scattered across the levels.