Half Life.
I used to have a Windows 98 PC and I would buy PC Gamer. I didn't have the internet back then but the discs that came with the magazine would contain a selection of mods. In particular my favourite was a single player mod named Half Life: Darkstar. The game had a lot of effort put into it with new dialogue and textures added rather than solely relying on existing assets. Sadly it ended on a cliff hanger and there was never a part 2 made.
There was a cool bit where you were shrunk and so one room became almost like a complete level.
The mod took place on a spaceship called Darkstar and you had to escape.
You can see the ship had it's own unique look from Black Mesa. Also, is that a new enemy?
If there are any retro PC gamers out there, I will say this game has quite a good length and high production values for a fan project.
Alternatively, I recommend just reading about this mod.