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.

The Tyriades seem to be in a battle amongst themselves as to Lea/112's role -- the combat Tyriades seem opposed to the Messenger Tyriades about this.

The only evidence of a Tyriad attack on the tanker is the corpse of a Tyriad (and marks on the walls) in the kitchen. I don't think the Tyriades attacked the tanker. I think that the chef used them (when the scientists were finished with them as research subjects) to put in the bouillibase.

I suspect the marks on the wall were the Tyriades trying to escape from the kitchen.

Remember the three men in protection suit in the inhalation chamber? One of them got a nasty wound at his side. it seems that it results from some big claw. And that bonus picture of this scene gives strongly such impression. That's why I got the impression of a Tyriades attack. On the other hand, it realy doesn't make sense that the RA troops killed their own agent, the chef. So I think he died in a Tyriades attack also.

I have to go back in to look at the wound you mention. Does Lea comment on it being made by a claw? If she says it was made by a claw, that would cinch the idea of a Tyriades attack, and some of my theories go out the window. What bonus picture -- I must have missed something! I don't remember Loyd mentioning the Tyriades attack when he talks to Lea -- I think he just talks about the RA. Though he isn't exactly in full possession of his senses by then.

As for killing their own men -- the RA organization is so decentralized and so ruthless that killing their own agent fits right in with the way they work, IMHO. Did you decode those RA files (the rather long ones) in (I think it was) Lincoln's sensitive files? The RA had penetrated the uppermost levels of government, and included some of Lincoln's own superiors. Lincoln had concluded that they were so powerful that EDEHN's only hope for survival was that they wouldn't be so ruthless as to take out their own -- which they finally did.

BTW -- wasn't there an RA logo on the helicopter that picks Lea up at the end of the game?

Yes, I decoded the RA files, and noticed the logo on the helicopter. It did give rise to another possibility. Do you think Lea is a member of RA? Such hypothesis did give her the immunity so that she could survived the RA attack. And other facts may support this hypothesis. In one of the files the security officer mentioned that Lea was considered for a promotion by the military superiors. In light of the fact that the RA had penetrated the high levels, this promotion could be an attempt to elevate a RA spy for their own convenience.

In another thought, could the RA logo just stand for "Rescue Agency"? I just can't make of some words in the "Outcome" cutscene-- "this is ??? rescue centre...."

Lea as an RA spy. That never occurred to me. Though I remember that she is rather high on the "suspect" list (one of them anyway).

Why would she then defuse the bomb? (Hmmm, of course she doesn't always defuse it, depending on the player.) I suppose she could go through the entire Tyriades world, including the "joining" that's only briefly alluded to, and then return if her job was just to observe and report back and not to actually sabotage anything.

Somehow I have a hard time thinking of her as an RA spy, though. She seems too kindhearted.

As for surviving the RA attack -- it's possible that the charm she wears around her neck was somehow protective. I think it's also possible that John Palmer (the one who wrote the letter at the beginning) figured out a way to jam the entrance door so that the RA couldn't get in.

I would definitely like some confirmation of either of these theories, though.

Obviously, at some point Lea volunteered to become a research subject and meant to go into the Tyriades world to contact 112. There is nothing in the files about this, though. Oddly, the emails seem to stop (as I recall) in mid-October, whereas the attack seems to have taken place in November. (Manchek's and Dimitrinko's codes last into November.) Why was everyone on the ship not emailing one another at the end? Was the email system down?

I guess the RA attack happened in mid-October. Manchek's codes is regular and deducible, just like Dimitrinko's agenda which could be made in advance. So they don't seem to contradict with the "mid-October" guess. And the mail system could have been down in the attack, so that we can't talk to Lea with it. There could be, however, some action going on in the tanker following the attack. The RA troops seemed to like lingering a bit, and took advantage of the installations of the base for their cause. Maybe this is the point at which Lea volunteered to receive the HO treatment as preparation for going down into to the Tyriades world. It's a RA act, thus there is nothing about it in the files.

As for the charm, I thought it was made by the Tyriades queen with help of 112, and handed to Lea by 112. But another theory seems more suitable now: the charm was created long time ago by the old Tyriades and human race, and keeped by the human race since then. It is the RA who holds the possession of the charm today, and also the only ones who hold the memory of the history of human and Tyriades. They are aware of the existence of the Prophecy; even they forgot it, the informations from the EDEHN base should have reminded them of it. At last they decided, maybe with some furious debate, considering there were some RA members looking forward to see the extinction of the Tyriades, to keep their end of this old bargain. They gave Lea the charm, and helped her fall into hibernation, so that she could help to fulfill the old prophecy 34 years later...

I always wondered why Lea never made any comment about the charm and her clothing when she waked up, acting just like there was nothing special about them. Maybe that's the answer. According this theory, the RA organization is not so ruthless, isn't it?

112's hands as he beats on the window of the inhalation tank because he's in pain -- and you can just see two shadowy shapes outside the tank, but I think it's clear those are the scientists trying to calm him down. I also took a look at the three corpses outside the inhalation chamber, and there's nothing there that would indicate a claw, at least not something that seemed obvious.

I think you are right that the Tyriades were informed that the RA might be planning an attack -- one of the scientists mentions that Lincoln (the security guy) went in to talk to the Tyriades. I suspect that his purpose was to warn the Tyriades about the RA, since Lincoln knew that none of his own superiors in the military would listen to him.

This might explain the sudden decision to get Lea ready to go into the Tyriades world, and might explain the messenger Tyriades figuring out a way to get the necklace/charm to Lea while she was preparing through inhalations to go down there. One of the stories called this charm "The Original Egg of the Convergence," and the info about it is that it both senses and emits hydroxide oxydrin, and that it was probably created by a Tyriades queen but designed by a human -- so maybe the charm WAS a collaboration between the current (soon to die) Tyriades queen and 112.

I'm wondering if Lincoln shut down the email system to keep the RA spy from communicating with the outside RA. I think the raid must have been November because the code that currently works for the bathysphere was a November code.

I enter with Miilyan.
A squad of Tyriades surround you.
You approach me.
We are alone at last for a few brief moments
How I’ve longed to see you again!
Ever since my awakening, and our first exchanges by two-way cameras, I’ve felt a presence.
You seem so different.
You’ve become one of them.
I have no regrets.
I had to see you one last time to conclude our story.
You ask me to stay with you.
I chose to go back to the human world.
And so, I leave this island and the Tyriades civilization behind me.
By my presence, the prophecy has been fulfilled.
112’s arrival in the Tyriades world will continue to create deep unrest.
I leave him now to encounter his fascinating destiny.

This has made me wonder if 112, over the intervening years, actually did "become one of them" -- fully mutate into a Tyriade.

an RA spy. I just can't quite believe it of her. When she wakes up, she thinks that the person operating the camera is a crew member -- if she had gone under the hydroxide oxydren inhalation scheme specifically to spy out the Tyriades realm for the RA, I think her first thought would have been that the person operating the camera would be from the RA, not a crew member. Also, if the RA wanted to send her into the Tyriades realm as a spy, why would they leave her there, unattended, for 34 years?

In fact, under any scenario -- for instance, that Lea was preparing to meet 112 and that he had sent her the charm -- it doesn't make sense that she just lies there for so long. Since it was 112 behind the cameras -- why did he wait several decades before contacting her?