There's a lot that I like about this - and I'll definitely be keeping an eye on it. As comments have already mentioned, there's some bugs and some misspellings / bad grammar, but what's already here looks genuinely like it could go somewhere great.
I ended up editing the actual .html file as a .txt in Notepad++ to fix some of the bugs I encountered, and here's some nitty-gritty details I found in the code (apologies in advance for any names or phrases I get wrong, it is a recurring problem that my brain reassembles wording in strange and unique ways):
1) as said previously, several instances where Stress is called to be lowered, yet the stat is increased - the easiest way I found to locate and fix these was using the Find (CTRL+F) function to find 'stress reduced' or whatever the exact language was and editing the + into a - at every appearance. Some of these look like they might be errors in the player-side description, rather than the engine-side math, however, so YMMV on which way to fix these.
2) as recommended, I started with the science vessel instead of the prison, and I rather quickly noticed there was no way forwards without getting raped. As personally I'm a hardcore romance fangirl, rather than sexual harassment (I know, strange choice of forums in that case), I poked around every event tree I could until I found out the one path that doesn't involve that - however, it is currently bugged and unavailable. If you board the pirate ship, look for weapons, kill the pirate, then proceed to the science vessel, lure the pirates away to create an opening - you are then supposed to be able to fight them there. However, you cannot actually do so, because it checks for the variable $sword rather than $haveSword - this is one of several instances I found of this in the code. Another (particularly egregious) example is the prison 'assist Dash' fight after hiding and then following - which not only also checks for the $sword variable, it also checks for the $gun variable instead of the $haveGun variable used elsewhere, and fails to close the /if statement correctly. Even further, it misses the one of the symbols required to correctly close the speech dialogues, meaning they error, and, as previously mentioned, links into another variant of the same 'follow into combat' scene if you choose to attack the Firemonger, rather than moving directly to combating the Firemonger.
3) further, about the $haveGun variable, there is currently only one way to acquire said gun - that being to kill the leader of the pirates and leave the rest alive. As far as I could see, all other variants of the scene did not set such a variable - and even going to the Hades/Prison first has no route to setting it. I did, however, enjoy seeing several instances in the code that called for a gun before being able to acquire one - that's a lovely bit of foresight/planning. Of note, I also recommend the run->combat->endure segment for pirate combat on the science vessel to set the $haveGun variable as well, given that you end up defeating several pirates in that ending, one of whom is stated to have a gun. As at this point all of the pirates have been gassed into unconsciousness, picking it up just in case seems like a natural flow - especially given the focus on it during the fight prior.
4) Additionally, as far as Sergeant Michael weirdness - yes, he discovers cum even if you've literally never been touched by anyone, but also: if, upon arriving at Hades, you hide->follow->talk->combat->kill Firemonger, you never actually meet Sergeant Michael in the Hades itself - you recruit all of the security guards directly from Commander Sarah (Sasha?). Despite this, the dialogue between the Ship-Avatar-Body and Sergeant Michael when you go to recruit the prison guards as security for the ship assumes the two have already met.
5) After setting the guards as security, traveling around the ship while armed has them confiscate your weapons and send them back to your room. This is followed by a prompt to build a Conference Room via the Robotics Bay in order to pass laws. Upon visiting the Robotics Bay, the upgrade is actually referred to as the Courtroom, and requires a total of 200 people in order to be made - a number unachievable without recruiting every single possible human in the first sector. Perhaps adding an alternate unlock trigger, or making the Conference Room a 'lesser' version of the Courtroom with lower requirements that can later be upgraded into the full thing?
6) Considering that Dash and his crew are basically all but stated stated to have more solid control of the Hades than the actual prison guards, in addition to being better armed (if the statement about how under-armed the prison guards are when first seeing them is anything to go by), it's a little odd that they're not also potential candidates for ship security - especially given Dash does not paint them with a particularly favorable brush, should you interact with him before ever meeting them. This isn't a particular gripe or anything, just felt like an interesting possible-consideration.
7) When encountering the scientists for the first time, they seem to regard you as an appliance more than a person - a statement backed up by the Ship-Avatar-Body even outright mentioning it. Despite that, if they're the only ones you recruit from the science station, they're actually quite respectful once aboard the ship for the most part. This isn't inherently a problem in the slightest - maybe they're a lot more favorably inclined with their views upon you since they've been rescued and put in essentially much better living quarters, along with having something resembling actual hope with the travel to the Last Star. Still, if that's the case, at least a brief passage on the topic I think would be a really nice touch.
8) Rebecca's (?) dad, the incest-rapist. An option to explicitly disable that event would be greatly appreciated, personally - I didn't check if hitting the 'Back' command after reading the warning disabled it in the future, but having separate buttons for 'I don't want this but might later' and 'actually, I never want this' would be a good idea I think. That shit's dark, and while I can understand it, I like more fluff and warm/fuzzy (again, I understand that probably makes me very much an odd one out in this forum), and it's a bit of a sudden jump from his previous appearances - could do with some disturbing-the-peace events to foreshadow it, perhaps. He also basically outright demands your schematics if you need repairs, and requests them if you don't, so I thought calling him would actually have an option to hand them over - potentially redacted in parts if anything in the Ship-Avatar-Body might be usable to bypass the AI requirement, given he's not exactly made a great AI rights impression, but potentially not. It felt a little odd that there wasn't an option to even reference that conversation - though I suppose that might be in one of the other possible call-events, as I didn't check all of them.
All in all, while I'm not sure this game's direction is one that'll end up particularly appealing to my personal tastes, I thought it was very well made overall - I wouldn't have written this long a comment if it didn't make a favorable enough impression on me that I wanted to see it polished and succeeding. Keep going - and write the story you want to write! If my suggestions don't line up with the story you want to tell, they're only suggestions - if the intended narrative and themes need to be bent to include them, doing so would only make things weaker overall, I think.