In the 25th century, mankind has colonized all known space. Earth became somewhat of an Empire, ruling over all the colonies, the Terran government known for its ruthless methods. Finally, the planet Omni could not bear the tyranny of Earth any longer. The military of the planet assembled an all-female special giant robot combat unit called "Power Dolls" ("dolls" standing for Detachment Of Limited Line Service), led by the lovely and athletic Hardy Newland. The battle for freedom begins!

Like other installments in the series, Power Dolls FX is a tactical turn-based strategy game. The player can customize the robots, replacing and upgrading their weapons, etc. Navigating the six robots on a top-down battle map, the player can attack enemies when they are in weapon range. Enemy units include other giant robots, tanks, ships, etc. There are two modes in the game: story mode and scenario mode. The story mode has the battles evolve in a linear fashion, with cut scenes between missions. In the scenario mode, the player is free to play any of the story mode scenarios in any order.