It is the year 0211 of the Celestial Calendar, two centuries after the Solar Unification War which brought all the nations of the Earth under the rule of high sovereign Princess Celestia. Technology has advanced greatly under the guidance of the immortal monarch, and humanity has taken its first steps into the stars.

After generations of relative peace and stability, the Earth Sphere is embroiled in a new conflict when High General Luna, dissatisfied with the complacency of her sister, forms a coalition of space colonies vying for an independent government on the moon. The rising tensions between the two sisters finally culminates in the bloody Selene Revolt, sparking the great and terrible Sister's War.

Twilight Sparkle is a graduate and prodigy of the Celestial Institute of Technological Research, and has spent the last three months helping to develop a new weapon for the Celestial Forces. A Mobile Suit utilizing the Compact Harmony Engine of her own design. When the Coalition launches a surprise attack on the project's research facility, Twilight is forced to sortie in the newly completed "Gundam", and discovers that this weapon- and this war- hide more secrets than she knows.