Seventy years after her father's death, Princess Umbra daughter to Commander Bolt and Princess Luna, seeks out a solution. The Griffin Kingdoms threaten war, but her mother and aunt refuse to fight. Unfortunately Princess Umbra who is sworn to protect what her father gave his life for, decided to take matters into her own hooves, claiming the throne, banishing her mother and aunt, and destroying her threat by establishing forced peace not only on The Griffin Kingdoms, but the entire world, and all with her new name, Thundaga.

However, five hundred years later, a pegasus names Cirrus emerges from Ponyville, and with him, a new hope, for he carries a power that he doesn't understand. Now he, an ancient dragon, an evil enchanter, and an ancient hero now must unite the nation and face the tyranny of Thundaga, and spread peace as was fabled by The Third Commander.

Pre-Story Comic The Ballad of Thundaga