A few decades prior to the events of the first Rosenkreuzstilette game, the Empire and the Church were known for having feared and persecuted Magi, those born with the gift of magic, throughout the world.
However, such an injustice sprung a man named Rosenkreuz to action, and he and his eight disciples stood up to them in a long and grueling holy war that ultimately cost Rosenkreuz his life. However, his wish was granted with his death, and the Empire allowed the Magi to live alongside its human soldiers as part of their military.
Over the decades that passed, however, such a peace didn't last, and it wasn't long before persecution began once more as contempt for the Magi's existence was too much for them to take.
But not willing to stand idly as the Empire brought them back down, disrespecting their beloved Rosenkreuz, the Magi launched a coup against the Empire. Graf Sepperin, the former leader of RKS at the time, ordered Freudia Neuwahl to lead the rebellion in an attempt to destroy it so that they'd make a peaceful new persecution-free world for Magi.
Of course, as pointed out by Spiritia Rosenberg, a training instructor for the Empire's army, the rebellion proved to not be the way to gain acceptance from it, and instead was only both a waste of time and a downer for the human/Magus relationship Interestingly, the part about the Empire's persecution of Magi wasn't actually the case at all.
The Church was actually afraid of Iris Sepperin after having learned of her being reincarnated from Rosenkreuz and born with tremendous power and great knowledge, along with her true nature, and, hoping to stop her from posing a threat to the world, sent several priests after her, but their attempts to kill her were foiled when she killed them all. Karl was also able to see through the "innocent girl" mask she wore to fool everyone else.
Iris learned of this and when he attempted to kill her as well, she told her father about his attempt on her life and manipulated him into imprisoning him within the castle prison. It was there that Sepperin believed that RKS was the target of persecution again, and that's how he had RKS launch the coup against the Empire, as orchestrated by Iris. RKS's rebellion was aborted once Tia and Freu learned of Iris' true nature and motives.
A few months afterwards, the Orthodox Church, in response to the rebellion that few months ago, oversaw the formation of the Schwarzkreuz and they began witch-hunting Magi. Unbeknownst to both the Empire and the Schwarzkreuz, however, Eifer Skute was manipulating them both by posing as a member of the Schwarzkreuz, as, in truth, she was actually a servant of Iris. Eifer eventually betrayed the Church and murdered the pope and revealed her true nature as well, and the Church and the Schwarzkreuz resigned.
- While it is by far different in nature, the Holy Empire is similar in appearance to Renaissance Era Italy.
- An unnamed priest that is presumably a member of the Orthodox Church makes a brief appearance in the beginning of Rosenkreuzstilette Grollschwert before he is killed by Iris.