The game's length is its most criticized feature but think about that in relation to the original film: the original film had you on the edge of your seat, as Ripley tried to escape from the now doomed Nostromo. Then the film pulls one last surprise as the Alien tries to kill her. Similarly, the game seems to end after the Alien is disposed of in Chapter 10, and the Reactor/Hive but keeps going. It's the perfect way to emulate the original film.
Additional brilliance also comes from the fact that you go through the same areas multiple times. This harkens back to the films, as the main hallways of the Nostromo was just one long set that was made to appear as different decks by changing the lighting. Essentially by having missions you go back and forth through the same areas previously explored, it utilizes the "sets" of the station in the same manner without having to have multiple distinct levels for gameplay (like other typical video games). It's making use of the limited settings to match the original film even more.
It also heightens the horror, especially as you revisit areas early in the game, before the Alien became an active threat, areas that were safe but aren't anymore. You're getting better and more efficient at navigating the station. . . but so is the Alien.
There was always a plot hole in Aliens that the colonists never picked up the signal that drew in Ripley's crew to the Space Jockey's ship. Take this game as canon and you have an answer: Marlow's crew turned the beacon off.
Why are paranoiacs so hostile towards you? Sometimes when you're spotted, someone will say "I don't know this one" or some such. The station had a population of 500 which meant that almost everyone knew everyone else - seeing a complete stranger probably freaks them out. That combined with the fact that you are carrying a lot of weapons probably unnerves them.
Combine that with the fact that the entire Xenomorph outbreak started because an unknown woman was allowed onboard from off-station, and their adverse reaction to a female they don't recognize starts looking pretty rational.
Why is the Alien so much more difficult to shake off in the hospital levels than in the Seesgson Synthetic level and, to a lesser extent, The Trap? The explosion must have injured it and it is recovering afterwards. Fridge Horror sets in when you realize that, as terrifying as the Alien is, it’s nowhere near as bad as could have been.
The flamethrower is the one thing that can drive the Alien off, but it still doesn't kill it. The flames are causing it pain, but no real harm. It's made of silicon, people — a.k.a, a substance that isn't known for its capability to burn.
Why is Amanda's breathing pattern so bad when she's holding her breath in the lockers? According to Aliens, she died of cancer. If this was lung cancer, then it explains the questionable breathing.
The whole story kicks off because the crew of the Anesidora found the blackbox of the Nostromo and accessed its records, leading to them going to LV-426. Anesidora is another name for Pandora. They opened Pandora's box.
Both Marlow and Waits are designed to be similar to Ripley in that they do whatever it takes to fight the Alien. However, a subtle element of their character is that they lack the positive traits of Ripley during the first film, such as her compassion and desire to help people. Both men become obsessed with stopping the Alien however they can, at the cost of their humanity. In a way, they become just like the Alien; a monster that kills anyone who gets in their way.
When you're outside, right at the end of the game, you can read the subtitles and see that Verlaine says she'll put the airlock on "auto", meaning it opened for an alien as soon as it got close to the Torrens. That is how the Alien got on at the end.
Samuels going to such lengths to try and salvage the situation, including putting his life on the line by trying to interface with APOLLO in a way Ripley describes as suicidally dangerous (and Samuels calmly agrees). But then, it's no surprise he'd do anything and everything to try and help once it becomes clear how dangerous Sevastopol is — it is against his programming to harm, or through omission of action allow to be harmed, a human being.
In the first few levels, you still see a decent amount of people, some not even armed, running around but by the last few levels you don't encounter anyone. When the androids became (more) hostile and the aliens spread throughout the station - both actions caused by you - this probably led to the vast majority of the remaining survivors being slaughtered. People that had survived a month of hell were killed at the 11th hour because of you.
Why are so many survivors hostile? The crisis has been ongoing for several weeks; at the beginning there probably were larger, more civilized groups of people - which would have been more likely to be open to attack from the alien and looters. Soon enough word would have gotten out that large groups are the most at risk. The horror sets in that the violent paranoiacs arguably have the right idea.
Furthermore, rumors of the aliens' life cycle would have spread throughout Sevastopol following Foster's death by a chestburster. By the time of Amanda's arrival, many of the survivors may have even witnessed the impregnation/chestbursting process firsthand due to the presence of facehuggers on the station. When paranoiacs attack Ripley, they are likely viewing her as either a current or future host for more of the monsters.
In Ellen's message to Amanda, she never actually clarifies that all of the Nostromo's crew was dead before she blew up the ship. It's possible that Amanda thought her mother killed her co-workers to get rid of the creature and is no better than Marlow- something Marlow certainly seems to believe ("If she was here, she'd be helping me!"). This would explain why she stopped looking for her ostensibly murderer of a mother. Also notice how in most of the latter chapters, Amanda's main objective is to escape from the station, because she already found her "closure", like what Samuels said at the beginning.
It's eventually revealed that the Alien has created a hive on the station and there are now a lot of the monsters roaming around. This begs the question of whether you were actually being stalked by just the one Xenomorph throughout the first half of the game, or a whole bunch of them, and nobody had even realised it soon because it's impossible to distinguish two Xenomorphs from one another.
Similarly, you might occasionally encounter a glitch where, for example, you can see the Xenomorph's drool dripping down from a ventilation duct above you, skirt around it and go through a door only to see the Xenomorph standing there. While still a glitch, it's one that makes perfect sense considering that there are multiple Xenomorphs on the station.
Think about when Ripley was in and around Sevastopol’s core and Anesidora’s exploding reactor. Regarding the former, all the Joes in the area have on haz-mat suits, which would suggest it was some kind of hazardous environment and the latter was turned into “a goddamn nuke”. Now think about the films where we find out that Amanda died of cancer at the relatively young age of 66 and never had any kids. Could that have had anything to do with the aforementioned levels? Could Amanda have gotten cancer and/or been rendered sterile during the events of the game?
It’s subtle, but watch Waits’ behavior during the first part of the level The Trap when you’re in the Systech Spire. He tells you the plan, what has to be done to achieve it and just tells you to “report in as you go.” When that plan fails, he comes up with another idea - conspicuously not telling you what it is - and sends you to Gemini Labs. Once there, Waits micro-manages you to each objective and even just rambles on about the lab’s background to the point that Amanda has to exasperatedly tell him “enough talking!” He’s trying to goad you into telling him to shut up so that he doesn’t have to divulge the final part of the plan - sacrificing you to get rid of the Alien.
You can find a recording from Hughes to his sleeping wife telling her he’ll be back before she wakes up. Since he never does, his wife and daughter must have spent however little time they had left wondering what happened to him. Or worse, they went to Seegson Communications trying to find him and instead found an army of killer robots.
When you think about it, the fate of Spedding and his secretary. His last words were to tell her that he loved her and thinking that she was safe. The poor woman was dead and only in his office because he put her there - while it’s unlikely she would’ve survived terribly long, she would’ve had more of a fighting chance than being locked in a room with 6 murderous androids.
According Word of God there was a Xenomorph Queen on the station. Considering how many eggs you come across in the nest, she must’ve been close to you - like one or two rooms away close.
In one of the later levels, you can hear eerie sounds in the distance unlike anything you've heard up to that point, even the presumed wails of the webbed-up victims in the hive. Those howls could easily be coming from the queen.
Some of the paranoiacs’ dialogue about eating (specifically, when they talk about how they were hungry “but never thought we’d have to resort to that ”) suggest that some of them have resorted to cannibalism or something similar. (Since they’re absolutely fine about killing you for just being in the same vicinity as them, we know they’re not just talking about shooting people for their food.)
Sometimes, after the Smash to Black screen, you can still hear Amanda gasping or screaming. Considering what happens in the 2nd half of the game, that would suggest instead of killing her outright, the alien was taking her back to their nest.
In a break room on your way to the Gemini labs module, you can come across a children's robot toy, along with a child's drawing of the Xenomorph. And later on, you encounter one of the logs that mention children being on board Sevastopol. This means that without a doubt, there were children who were probably taken away or killed by the Xenomorphs, and Sinclair's last audio log only confirms this.
When you finally meet Waits in his office (the only of few moments in the game you can actually breathe easy and feel sane talking calmly to living people), he briefs you on his plan to capture the Alien. You will also talk to Marlow, who's in his cell. Then you get the flamethrower and before you're ready for another action, you want to save your progress on a save station in the office. But what is that? When you point to it, it shows disconcerting text Save progress - HOSTILES NEARBY. You start panicking a little, but it is safe to say, nothing can hurt or kill you in this location. No alien, no robots, no facehuggers, nothing. Sure, you could ascribe the warning to the Marlow, the not very sane man. But it could also be warning you about Waitshimself, as he secretly wants to sacrifice you to the alien.
It's been noted that part of what makes the game so tense, so scary, and so good is that, as you play and evade the Alien, it seems to develop a personal enmity for you, annoyed that you've escaped its clutches so many times. With the reveal that there are multiple Aliens, and that you weren't necessarily being pursued by the same one even before Gemini Labs, that goes out the window, since they can't all have personal enmity for Amanda, right? Wrong! While the series hasn't come down on this conclusively, it's widely believed (and canon in some stories) that the Aliens have telepathic communication, the entire hive coordinated by sharing thoughts, perhaps even a full-fledged Hive Mind. So yes, every Drone on Sevastopol is, in a way, the one you keep eluding, and is increasingly eager to hunt you down specifically and make the kill.
The Alien behavior is rather odd compared to their established pattern in other media. The RPG wouldn't come out for a few more years, but would establish that once a Queen is in place, Xenomorphs enter the "hive" stage and smooth-domed Drones become ridged-skulled Soldiers, yet you only see Drones. The Aliens have also historically favored Zerg Rush tactics once there are enough of them, not sending out lone scouts (to the point no one suspects there's more than one on the station until Ripley finds the hive). Yet the Aliens are nothing if not adaptable, mutable almost by their very nature. Perhaps keeping the bulk of the Drones close to the nest and Drones not molting into Soldiers is a response triggered by something unique to Sevastopol. Perhaps they knew, somehow, the station was unsuitable for a long-term hive, and the drones were prepared to hitchhike on any rescue ships that arrived. Or perhaps they were just on the cusp of transition to a full hive, the Drones almost ready to start molting, when Ripley triggered the reactor purge, which probably killed the Queen and meant the Drones needed to start almost all over again. If the latter is true, this adds a dose of Fridge Horror: Soldiers are a lot tougher and more coordinated than Drones. Bad as the Drones you had to deal with are, it could have been so much worse.
