Miss Quill's genocidal heirloom spell — a three-generation working to slaughter all of the Over City but the flyers.
The Final War is the grand purpose behind everything on the third floor's settlement: a three-part 'heirloom' spell first cast by Miss-Quill's grandfather, continued by her mother, and meant to be completed by Quill herself. Its final act is a long, dangerous casting spread over three nights, demanding thousands of mana points — which is why Quill built her Krasue army, harvested souls, and turned her dead husband Remex into a soul capacitor. On completion, unleashed beasts would sweep across the Over City and kill everyone except those whose essence Quill had 'protected' by collecting their feathers — the Skyfowl, the Chickadees, and their families — reclaiming the ruined city for the flyers she believed rightful rulers.
Remex likens it to Scolopendra's nine-tier attack that once ruined their kingdom. Quill had already cast the first night and begun the second when Carl killed her — leaving the half-cast spell to misfire catastrophically.
The apocalyptic conspiracy driving the murdered-prostitutes quest — a slow-motion genocide interrupted only by Quill's accidental death.