1. What We Know So Far

What do we know so far?

The inescapable conclusion is that Daedalus - Penumbra's puppet - is aware of Xenon and the Academy, and is maneuvering itself into a position to crush it and simultaneously propel itself into power.

The second inescapable conclusion is that Daedalus is somehow in knowing or unknowing collusion with Chernobyl. It's the only way they could have gotten that information about Xenon's organization. This may be a master plot by Chernobyl, or mind-control via Charlotta, or outright cooperation. The last part is unlikely, given that Chernobyl stole an important Daedalus prototype several months ago; why would he steal what he could have asked for outright? Nonetheless, some sort of machinations are at work.