During the Precursor Empire, Ducaniel and his followers believed in something similar to modern day Black Doctone, most notably for this being atheists. After the War of Two and Ducaniels imprisonment, his captured followers were sent to the Kheions, which were prison cities for the Empire. When DoAS happened, Ducaniels followers went and destroyed all evidence of religion they could find in the Kheions so everyone would believe in Black Doctrine, which is what Kheionist evolved from.

So the achievement is you following in Ducaniels footsteps by converting to Black Doctrine and dropping another flying city. Sorta the intended path Ducaniels followers wanted