As the years after the Miracle at Zend passed, the situation on Zend worsened. While the United Empire ruthlessely crushed suspected cultists at every chance, the Republic made the mistake of taking a more humane approach. The cult continued to fester in the shadows of the Republic, and the cultists became bolder and more militant. Bombings and terrorist attacks began to sprinkle the map, and cult leaders started to speak of "revolution," and a "cleansing" of the Republic. The covert agitators employed by the Empire significantly worsened the situation. (Given the choice between torture/death and radical preaching, arrested cultists almost universally chose the latter option.)
Eventually, a full scale rebellion broke out. The rebels, with their widespread infiltration, quickly seized control of Zend. The violence was great, with atrocities committed in the name of purity. However, the massacre of Sophon residents proved to be the far most damaging event.
In 3731, after three years of bloodshed, the Republic ordered an end to tolerance of the cult. The first major task of the Republic's new spy organization, Black Star, Anomorro was assassinated by operatives disguised as temple worshippers that pricked him with a poison dart while he was giving a lecture to new students.
Soon after the assassination, the Rebellion began to crumble as many high ranking priests brought their claims forward and philosophical debates began in earnest. No suitable agreement was made about just what Zend would have wanted for the Republic, or how to begin ascending to his tier of godhood. The cult's communication network broke down and soon the Rebellion had been reigned in and controlled.
Republic loses diplomatic relations with the Sophons, Followers of Zend becomes a major, if fractured, religion among the Republic's people. Black Star proves its worth as the Republic's intrigue specialists.
(Thanks to Javarino)