Your theories on why... (2.8 Spoilers)
Helios was cultivating bio weapons. Or at least, that's what the results of their research currently look like.
Between Seed's and Phaethon's abilities, the latter's description in the boss file, and the staff crashing out during the Blazewood dream sequence, it does seem very possible that the Academy was a pretty shady institution outside of specific individuals like Carole. Fundamentally good-natured people doing terrible things for terrible organizations is a recurring theme in ZZZ after all, see Eve, Billy, Harumasa's doctor and, most notably, Carole herself while working with the Exaltists.
So, what was their MO? Assuming the Exaltist attack wasn't an inside job to some degree, it seems rather unlikely they were directly aligned with the Creator, for instance. All we know of so far is their nebulous slogan, "catching the sun", whatever that sun would be.