These are the plot notes I took for after the Council of the Generals, for people who couldn't get past it.

In broad strokes -- YOU are 112 and have been guiding Lea out of the ship and into the Tyriades world. How you have done this is not specified -- can you control everything remotely from the Tyriades realm? Or have you actually left the Tyriades realm to come to the ship? (I favor the latter theory because of the opening sequence which I think shows 112 traveling via the Wind Well/Abyss.)

The Messenger Tyriades, your friends, are at war with the Combat Tyriades. The Queen of the Tyriades, who lives for 700 years, is about to die and to be replaced by a new Queen. The prophecy that the Tyriades and humans will converge to form a new species will be fulfilled by 112 somehow (how isn't specified) and it is important that Lea make it all the way to a cave where he is waiting to see her in person, as this also fulfills a prophecy.

Anyway, after the Council of the Generals there is a battle between the Messenger and Combat Tyriades -- Lea ends up near the bomb which she either does or doesn't diffuse.

After that the Messenger Tyriade you've met before (Miilyan)takes you to the Abyss where you program your trip to meet 112 in person. That's the last puzzle.

Suddenly you reach the final cutscene -- Lea is back on the deck of the ship, being picked up by a helicopter. She says that she saw 112, that he asked her to stay with him permanently, but that she chose instead to return to the human world. So the Messenger Tyriades got her back to the ship and somehow alerted the authorities to pick her up.

Lea says that she has no regrets, and that she's sure 112 will lead a fascinating existence in the world of the Tyriades.

That's how the game ends.

As for your question -- is 112 human or critter? My answer: well, both actually. That's my interpretation, anyway. 112 had realized that he was part of the future of a way to build a bridge between Tyriades and humans. He made a decision to sacrifice his human future to stay with the Tyriades. He spent so much time with the Tyriades, he partially mutated into one of them.

He still had the ability to communicate with humans. And Lea did eventually get to meet him near the end of the game and he asked her to remain with him. But something about him (probably his appearance after the mutations) was so shocking to Lea that she chose to return to the human world after spending the entire game practically killing herself in order to see him one more time.

where the necklace that Lea wears came from? And why she survived the attack on the ship when she couldn't even hide or defend herself?

There are evidences that suggest the tanker base was probably raided by Tyriades, just when the RA troop attacked the base. I wonder whether the timing has anything to do with Nichols. The Tyriades may, with their awareness of the role of Nichols in the prophecy, take action to protect her from the RA troop's assault. If that's the case, they might very well make other arrangement to help Nichols play her role, for example the hibernation, and giving the charm/necklace to her. It's the Tyriades who'd like to see the fulfillment of the prophecy after all. Of course 112 plays a key role behind all of these. May be he is the one who left the message by Nichols' bed.