Ellen Maracheck is referenced as the host for Subject 82599 "Nay," but Teah finds her still in a stasis pod, and is apparently surprised by her ... condition. (If she'd known Ellen was dead before that, she wouldn't have reacted, so as not to alarm John.) When we see Ellen at the end, she's mummified and has been dead for months, probably. John sealed her pod before putting her on the ship, so he knew she was dead and just wanted to die on the Groomlake instead of escaping himself, as a man without family.

So, how was Ellen being used as a super Soldier host, and long-dead in a failed pod?

(Side note: Frederick and Nay's reports are labeled "Lana" when opened.)

Far be it for me to redirect to GOGs competition, but there is a very detailed discussion on the ending at the steam forum: http://steamcommunity.com/app/380150/discussions/0/527273789697288051/

Never heard of Richard, really interesting, thanks :)!

Great response, awalterj, and thanks for the link, Chris/Nic. =) I didn't disappear, I've just had a lot to follow up on. Since your posts, I've read the full steam thread, which led to the Game Devs Play Games Stasis series, which I watched through in its entirety, and then found an additional deep discussion (if somewhat critical at points) in the comments of Part 12 of Nokzen's super high-quality silent playthrough here. Oh, and then I had to track down David Perry on Game Design and 8-point plot structure. Really, guys. ;)

I'm going to try really hard not to write a giant essay here, so grade me on succinctness, please, if not brevity. =) Mostly I'm trying to articulate the remaining conundrums.

Chris confirmed that it's been three years since John was taken, and about three months since things went to hell. Someone was tripped up by how long some equipment had gone without maintenance, but I'm pretty sure that stems from the Groomlake's previous life as The Tower. Ellen and Rebecca were both platinum blonde when they went into stasis originally: Ellen's corpse still was at the end, but Rebecca wound up ... maybe younger with maybe darker hair by the time of her death. Chris says the ambiguity was on purpose.

Chris also confirmed that John is not a clone, Te'ah found Ellen already dead in the stasis pod (which is what it sounded like in the voiceover), and Rebecca really died. He also called the Game Devs Play Games commentary analysis of the ending "brilliant," so you can imagine much of what they said is correct or nearly so. So, what did they say?

Paraphrased: John changed the shuttle's destination to his home planet or somewhere no one would find her bone marrow for research, expecting someone will find her and revive and and all's well. But, Ellen was dead the whole time.We were actually alone this whole time, and John dying by himself in the Groomlake is the perfect embodiment. Rebecca's fate was sealed, Ellen was dead, and John's been alone this whole time.

I thought most of that was pretty self-evident, which is probably good since Chris blessed off on it ... minus the initial expectation that someone would find Ellen and revive her, because I'm not at all certain what state John thought Ellen was in. There seems to be very little consensus/certainty/evidence one way or the other, at least that's been expressed online where I could find it. I'm sort of inclined to think John knew she was dead, and sent her off for him to die alone.

Now, where he sent her .... I'm really not sure ... John's a compassionate man, and he lamented a couple times in the course of the game that, as horrible as the work done on the Groomlake was, it was another tragedy on top of it to think that all of it would be for nothing. Despite the GDPG perspective above, he could theoretically have redirected the shuttle somewhere the data in Ellen's marrow would be found and used for good, but not by Cayne nor whoever Te'ah was sending it to.

So, back to Ellen and Rebecca. We have a collection of weird facts:

() Ellen was the best host and was used for breeding;
() Ellen was dead in a stasis pod throughout the story;
() three years had passed since the Marachek's capture;
() there were three identical pregnant women in the breeding room (with oddly distended giraffe necks);
() John still hopes to find Ellen alive *after* killing the pregnant women;
() John still hopes to find *Rebecca* alive after killing the pregnant women;
() the Rebecca John finds may be younger than the girl he put into stasis, with different hair;
() John speaks tenderly toward the pregnant women, and recalls Rebecca's lullaby.

No one's sure how to reconcile the fact that Ellen was being used for breeding with the fact that she was found dead in a Stasis pod. I could hypothesize that she was taken out, found to be an amazing host, and then cloned and put back into stasis (which subsequently failed). We know clones' growth could be accelerated, so the pregnant women could have been clones of Ellen or Rebecca. Regardless, John must have known they were clones because he thought Ellen and Rebecca were both still alive even after killing them.

Can anyone take these facts (and any missing ones) and create a sensible whole from them?

Heck, at the beginning of the game Rebecca asked John and Ellen if it was true that if you a had a bad dream and couldn't wake up, you'd be stuck in it forever. For all we know everyone else is doing just lovely, thank you for asking, and John's trapped, unconscious, in his personal hell. =)

PS: How about no one's even attempting to decipher the meaning or relevance of the disembodied psycho rhymes you encounter on two occasions? (Pardon my dubious transcription skills.)

[Male Sleeping Quarters]
[i]Mother had a lung that was covered in fat
Father had a tongue that twizzled so black
They didn't care for us
We didn't care for them
And so it happened again and again
Skin like a crocodile and eyes like sin
The allergy consumed them from within[/i]

[Medical Reception]
[i][informed the wound?]
I remember again
It crawled through the night and then and then
They corrupted their eyes
And tore through my skin
I'll never ever never again
They came for our mothers and then for our kin
changing God's work a sea to begin
We burned them with fire and killed them with men
Let us remember never again[/i]

... who is the speaker? Is the first one referring to the fungal infection? How does a tongue twizzle blackly? How many of the words above were actually what the voice actor read? ;)

A careful read of the diaries of DesSantos may firm up some ideas you have posted, all and all a great write up!