Back in late 1990s, after Internet but before CD-sized games being pirated over the Internet, I had a PC game which has been on my mind for a long time. It had a very graphically interesting opening sequence in many ways similar to the Amiga (and others) game Another World in terms of ambiance; the color palette being very dark with lots of dark blue and purple. You were not teleported to another world from Earth but rather in the future and space from the start, but ended up captured by either some alien race but humanoid shaped or other humans (your foes) but them wearing armor and visually distinguished from your appearance.
After the intro, you ended up in a prison cell and had to figure out how to escape. You were sitting down on a bench and you were the only occupant of the cell. In the middle of the screen and the center of the wall was a barred prison window and you could see things on the outside, possibly your foes/alien race working on this supposed military complex with prison. The prison door was most probably on the right side of the screen. I remember clearly that the only way I found was an air duct on the top of the left side of the screen which I was able to squeeze into. Once there, the scene changed to me crawling on my knees inside the duct. There is only one path but about halfway there is a spinning fan on the "floor" of the duct which shreds you to bits if you try to pass it. Your shredded intestines were of course purple and not red. I never made it past this second screen as I could not defeat the fan. It's possible the fan was never defeatable and that there was another way out from the cell in the first place.
There was a weapon-shaped object which the main character was somehow in possession of, but I was never able to fire it. It looked like an extremely low polygon count minigun; think 30 liter sized box for main body with one or two crude handles and a cylinder sticking out for a barrel. I was never able to fire it. Perhaps ammo was to be found later in the game? The weapon was disproportionally large compared to the main character.
Technically, it was pre-rendered or hand-drawn 3D environments with characters being low polygon 3D, very similar to Alone in the Dark but the backgrounds being far more reminiscent of Another World pixel style graphics and far less attempt-at-photo-realistic Alone in the Dark. The backgrounds would not move, it was just scene transitions from one room to the next, Alone in the Dark or Resident Evil style.
Despite having a Creative Sound Blaster and not a clone which would sometimes cause compatibility issues in the 90s era DOS games, I did not get sound and/or music working on this one. I was very computer savvy at the time so any DOS installer with manually setting up IRQ, DMA and such would not stop me, nor tweak any setup files manually or trying a lot of things to get around these kind of issues. I still never got it to work. It would for sure come with a DOS installer, but it may have been possible to run it under Windows. It was a bit too early in the "game" for crack groups to start stripping FMVs, compressing music and similar of CD-sized games for internet pirate distribution and music and sound being lost there.
The game most probably was keyboard controlled.
The game was very reminiscent of Another World in terms of color, style, prison, low-poly 3D (intro only of AW) and super interesting intro. I include some screenshots from Another world to get the color palette, but you need to mentally add more purple.
What was the game?
EDIT: 1995 BioForge did pop up after extensive searching. Intro with landing spaceship and waking up in a prison cell matches well as well as the 3D-character in 2D background type of gameplay, but visuals are way off.
EDIT2: I made a table of all your wonderful suggestions. Please let me know if I missed any.
More visual cues would perhaps be VirtuaVerse from 2020. The pixels are perhaps a little bit too large (it tries to look like SpaceQuest) for the presumed 640x480 resolution but color scheme and art style looks like something from the game.
