Short version: Add a mechanic called the Typhoon, a galactic Dust storm, using the strong gameplay of Winter in the Shifters expansion of Endless Legend. Tie it to Religious politics and the Academy superquest.


The rest of this idea regards potential particulars, not an absolutely necessary implementation.


Spoilers for the bigger twists here


Typhoon: The Typhoon reduces certain resource incomes, particularly Trade Routes and an Approval malus. Food malus would likely be frustrating due to loss of endangered populations, while a Science malus may slow the game yet would also be strongly thematic in the Scientist/Religious divide over Isyander’s actions.


Pearls/Motes: While a new resource may be more appropriate to create distance from the Winter mechanic, Pearls may still be appropriate, as they would strengthen the indication that Auriga is one of the Lost and suggest that Pearls are somehow common to the Lost, creating a thematic and mechanical tie. However, Motes of Dust may be more appropriate to the overall concept of a recurring Dust Typhoon, possibly being the early stages of regenerating Lost bodies.


Academy Mechanics: With Heroes and their bonuses not being afflicted by the Typhoon, there is a slightly stronger connection to the Academy; the Academy also might serve as the only source of Pearls on a passive basis. With Pearls only having a set supply all game, the ability to passively produce them would be a strong incentive to fight over the Academy.


Academy Plot: With the Typhoon being the aftershocks of Isyander’s secret efforts to return the Lost, and possibly related to the explosion of the Grey Owl, the Scientist ending would have as its reward the elimination of the Typhoon, allowing Science factions to deny further Pearl development to Religious factions; the Religious ending would result in more frequent Typhoons or a permanent low intensity Typhoon, the disastrous result of Isyander’s plan, allowing them to abuse their Religious laws. Academy quests would generally reward Pearls instead of Strategic/Luxury Resources.


Religious Politics: Currently a very strong but thematically disjointed party, the Religious party would now revolve around the Typhoon, as its effects would likely be considered religiously important in most belief systems in the galaxy. Religious laws would provide additional effects during the Typhoon or related to Pearls, as the player manages the faith and fervor of their people in the face of such an epic event.