Several decades after the Holy War's end, the RKS declared war on the Holy Empire and Orthodox Church, claiming that the Empire had begun persecution of Magi anew and disrespected their former leader Rosenkreuz. The current leader, Michael Zeppelin, commanded Freudia Neuwahl to lead the rebellion, starting with the burning of the Black Forest, in an attempt to destroy the Empire. The stated purpose of the rebellion was to destroy the Empire so that no one can stand in the way of the RKS's dream of a world where Magi can live free of fear and persecution. Spiritia Rosenberg was opposed to the idea of open war against the Empire, as she did not tolerate the sacrifice of innocents and knew of the consequences that would befall the RKS if she joined them in their rebellion, so she took it upon herself to stop the rebellion from breaking out.
Unbeknownst to Spiritia or the other members of the RKS, the RKS Rebellion had actually been instigated by Iris Zeppelin, Count Zeppelin's daughter, for her own amusement. Kahl Palesch had discovered her plans and attempted to kill her, but Iris framed him as an agent of the Church and told Zeppelin that the Church had learned of her power through him, leading to his imprisonment in the castle dungeon. From there, she tricked her father into believing that the Church would turn on RKS, leading Zeppelin to make a pact with the Devil to learn forbidden magic. It was out of his belief that the RKS was the target of persecution and out of desire to protect Iris from the wrath of the Church that he decided to launch the coup against the Empire.
The rebellion was ultimately aborted when everyone realized that Iris was the true culprit behind the rebellion's cause, and that the rebellion proved to not be the way to gain acceptance from the Empire. A few months after the rebellion, the Church began truly witch-hunting Magi again, these hunts lead by the mysterious Schwarzkreuz.