In Rosenkreuzstilette, the player takes control of Spiritia Rosenberg in traditional Mega Man fashion; navigating through enemy and trap laden stages, defeating the stage's boss at the end of each stage (in Rosenkreuzstilette's case, each of Spiritia's fellow Magi in the RKS) to copy their powers and using that very power against a boss who could be weak against it.

Having recently completed a six-month-long teaching assignment for the Holy Empire, Spiritia Rosenberg was anxious to return home to her friends and get some well-deserved rest.

Unfortunately, her homecoming would not be the warm welcome she had expected. As Spiritia returned to the Imperial Training Grounds, a monstrous dragon appeared and whisked away her student Iris, the daughter of the esteemed Count Michael Zeppelin. Moments later, flames engulfed the training grounds and its surroundings, ruthlessly consuming everything in their wake. With no time to lose, Spiritia and her fairy companion Lilli rushed into the burning forest in pursuit.

Making her way through the roaring flames, Spiritia was overjoyed to find her best friend, the cool and collected Freudia Neuwahl, already on the scene. However, her joy quickly turned to horror as she learned the identity of the arsonists; her own organization of magicians, Rosenkreuzstilette, with Freudia herself leading the assault.

Freudia informed Spiritia of the unit's decision to rise against the injustices fostered by the Empire, inviting her to rejoin their comrades as they declared war on mankind. Not one to tolerate the suffering of innocents, Spiritia refused - and vowed to stop her comrades from making a senseless and deadly mistake.

Join Spiritia in her quest to stop Rosenkreuzstilette, a company of rogue magicians led by Count Zeppelin himself. A squad composed entirely of Spiritia's dearest friends...