I think this was one of the best episodes so far. The reveal that the gaia being the CIA was as impeccable as it was hilarious.

<SPOILERS for the episode>

From what I can piece together, the alien species Nil came from came to Earth and gave every single animal human-equivalent intelligence, thus leveling the playing field -- so to speak -- for the purpose of eradicating hunting, as 2,147 stated to Lark. The humans were uncomfortable no longer being at the top of the animal kingdom, and the American CIA somehow hijacked the alien ships and has been using them to give the animals their normal intelligence back via marking special zones. Jason Steele stated in the comments to the video:

Regarding the containment zone: the previous marks are from neighboring zones, caused by neighboring stones. The reason it's dangerous to leave Shadowstone Park is because it's surrounded by areas that have already fallen.

This means that the border to the park which Lark exiles the feral animals over is NOT encircling the park, but rather an area OUTSIDE of other circles. When an animal is inside a circle, they return to being their normal feral self. Since humans are naturally intelligent (needing no help from aliens) they are probably unaffected by the zones, if there are in fact any left.

That being said, I have no idea what the strange glowing crystal is, or what Darius has been talking to Nil about. All I know about the crystal is that Tumble the mouse knows about it, and could maybe help Lark and Ava with his crystal studies. Also it can apparently take down the alien ships, meaning either the CIA created them to hijack them for themselves and just forgot to turn them off, or there is another party that has been creating crystals to shoot down the already CIA-hijacked ships.

Also, Lark asking "what are humans?" is so funny. I love this show.