Alternative Character Interpretation: Benny's homosexuality was kept out of the script, with the only reference being that someone found out his "secret". It gave Pat the impression that his secret was actually that he was a cannibal. Which he would have been, if not for the scene of him eating a baby being cut from the final version of the game.
Angst? What Angst?: The boy in Benny's scenario, who never mentions his mother again after learning of her tragic death.
Also Ellen is snarky as hell despite having suffered through 109 years of torture.
Anti-Climax Boss: The Yellow Rapist in Ellen's scenario. All you have to do is select a dialogue option where Ellen stands up to him, and he falls apart after one strike.
That may have been the point. For all its power, AM does not have the ability to resurrect the dead. It can only create illusions of people, and some of these illusions would just fall apart if attacked. AM thought it could just scare Ellen into submission with an illusion of her rapist, but it did not take into account that she could fight back against her rapist.
Complete Monster: AM, from both the story and the game, is an evil master computer who has already killed all but 5 members of humanity by the time the story opens. AM keeps the survivors mutated and twisted so he may torture them helplessly as he desires. AM forces them to wander, changing the environment so they can never get used to it and subjects them to hideously twisted torments (for example, he traps Ellen in a virtual reality simulation of the elevator where, years earlier, she was tortured and raped by a psychopath disguised as a repairman-with a simulation of the "repairman"). When one of them finally rescues the others by killing them, AM transforms him into a sentient blob, not even leaving him a mouth to scream with.
Darkness-Induced Audience Apathy: The story takes place in a nightmarish apocalyptic future where the only five survivors of the human race exist only to be mercilessly tortured by an irredeemably evil omnipotent supercomputer that can never truly be defeated. The entire "quest" that the characters undertake amounts to nothing more than an attempt to make their torture slightly less miserable for a day. It still fails. Bottom line: there isn't a lot of hope in this story, which cheapens the reading experience for some people.
The best ending of the game version, however, ends with AM defeated, 4 of the 5 survivors dead and at peace, and the remainder taking AM's place watching over the system, saying he/she doesn't mind the job and will slowly rebuild humanity using the colony on the moon.Good luck getting it without a walkthrough though.
Esoteric Happy Ending: Ted actually manages to triumph over AM and prove the computer is not the all-powerful god it set itself up as by killing all the other prisoners and freeing them from their torment. A combination of the fact that the price of this is being turned into a helpless jelly-thing to prevent him from ever winning again, and the fact that he's an Unreliable Narrator who's become too cowed by AM to realize he won tends to hide the "happy" part from most readers.
Oh, and there's the fact that for all the Moral Event Horizon AM crossed, it manages to get off with little more than a bruised ego.
Averted for the most part in the game's best ending however. At best, it's a Bittersweet Ending
"Funny Aneurysm" Moment: Ellen's phobia of the colour yellow (xanthophobia) appears to be just a silly thing for a grown woman to be scared of, and may evoke a laugh or two towards her encounter with the continuous yellow motifs that torments her during Ellen's scenario. Then comes the reason why she's so terrified of the colour yellow once you enter the sarcophagus posing as an elevator. In the past she was working late shift and entered an elevator, only for a maintenance man in a distinctively yellow raincoat to enter the elevator, lock the door, and proceed to attack and rape Ellen. For several hours. Then AM recreates the scenario inside the elevator again to torment Ellen even further with the same rapist wearing the same yellow coat from before.
Guide Dang It: It's a DOS adventure game from the mid-90s so this could be a given, but many puzzles seem to rely on not missing tiny pixels that represent items that you wouldn't know about. Gorrister and Nimdok's scenarios are particularly bad with this, because you can easily beat their scenarios and go to the endgame without even knowing you missed a step to get their best ending.
Inferred Holocaust: In the good ending to his scenario, the Scientist Prisoner escapes alive thanks to Nimdok's intervention. However, given that he's based on a real person from Nimdok's past, and it's established that Nimdok had no intention of helping him during his time in the concentration camp, it's very likely that he died in reality.
Jerkass Woobie: Everyone. Including A.M., if you consider his predicament.
Moral Event Horizon: AM has sailed way past this line, and his tortures allow him to skip over it repeatedly.
If Edna hadn't crossed it by driving her daughter insane, she certainly had by poisoning Gorrister and carve out his heart. Gorrister lived, but she was willing to do all that to escape.
Nimdok sold out his Jewish parents to the Nazis, and engaged in highly twisted experiments that mutilated thousands. In-universe, his former colleague tells him he crossed this long ago, and deserves punishment no matter what he does in the scenario.
The Untwist: Nimdok is a former Nazi. If you know who Dr. Mengele is than you'll figure it out before the intro cutscene is over. Even if you don't the imagery and dialogue in Nimdok's scenario makes it painfully obvious long before Nimdok himself puts 2 and 2 together.
Although the fact that Nimdok was also a Jewish man who apparently saved himself by giving his parents over to the Nazis seems to be the real twist.
What an Idiot: Ellen's inability to drink the water from the fountain. She says it's because she can't reach, but the fountain is only a few inches deep, and when she finally gets the cup, she has to bend down and scoop the water up the exact same way. Even if she somehow couldn't do that because it's too shallow, it's a fountain. There's a jet of falling water from the top of it.
In the opening scene, Benny and Ted could've easily dodged the tortures AM was inflicting on them just by sitting down. It is probable that AM could easily replace the torture with a less-dodgable one, but they would have a moment's respite.
Fridge Brilliance: Ted and Benny's tortures are designed to exploit their sense of self. Benny is being deliberately dehumanized, changed into an ape-like creature and being kept in a cage; walking (or at least, standing) upright is the only truly human thing he can still do, so if he sits or lies down, he's basically admitting defeat. Ted's a narcissist, so it doesn't matter if he sits down or not, he can't help looking at himself.
The Woobie: Who cares about anything bad that they've done. C'mon, how could you not feel sorry for them?