I stll don't understand what's happening
I'm only like 2 or 3 eps ahead of this, so I don't really get it either, but essentially, what I've gathered is that the planet is a living, breathing organism. The L.F.O.s and the Coralians (such as Anemone and Eureka) are humanoid cyborgs and organisms, respectfully, created by the planet and sent to the humans to see what they "do" with them.
The planet just was bombarded with weapons, and had an immune response at the site of trauma.
I think that's it.
The Scrub Coral are subterranean creatures that act as the protectors of the planet.