[FatPianoBoy]

Everyone's throwing out theories, and they're hitting all around what I'm thinking without actually hitting it, so I guess I'll chuck in mine.

Spoiler for $0.02:

I would say that the Blue was a prototype delivery system for a test-phase Thought-Arresting Weapon. That would at least explain the natives turning on one another. Also, that's exactly what Mentar's translation suggests.
This being a test, things are liable to go wrong, and they obviously did, which led to the explosions on the Blue.
This would also explain Onomil's appearance to Ekaril: she would be an Emiru-force manifestation of Ekaril's thoughts.
The tsunami was either the result of the shockwave from the explosions on the Blue or a cover-up mechanism deployed by Shivaril. It may also explain how one would hide 200 dead aliens from the government.
Mari still remains an anomaly, though.