Cuttlefish That Loves Diving
Theory: What if the Eight Research Institute and it's previous members made a deal with the "Gods". We will release the heartless disease causing massive destruction. Which will allow a new beginning where the Gods are the supreme rulers and not humans. that is why they are going out there way to destroy evidence. In return the Eight Institute are like a byproduct ruler.
At least some of the "gods" seem like they're keeping the heartless disease at bay. From the underground ark history, it seems like there was no sea of origins, mind corridor, etc...early on. Imagine if it there was no 3 gifts 1 price, but random abilities or all at once. I predict the Kalendaria are keeping the world at balance now and the 8th research institute is trying to make sure no one knows how it all works. They probably believe they are stopping another Armageddon by keeping everyone ignorant. They need to make everyone believe and fear the Kalendaria as "gods" and that this current ordered religous method is the only way to awaken and find the New World.