Looking really good! It also made me realize how long it's been since I actually played a typical FPS, and how audibly I suck now.
I pretty much agree with what obsidian said about the first two rooms (and about the screenie, obviously). I liked the attention to detail and solid texture use and mostly good lighting and various bits of eye-candy (e.g. mechanical bits, fans, gas/smoke stuff, etc.).
I found the shards under the stairs, and was wondering if there was other stuff like that I missed? Hidden goodies are great. I also wouldn't have minded a bit more health on the heal station, but maybe I just need to play better.
A few pics:

This guy got stuck trying to walk under/around the slanted pipe and just stood there walking in place until I got really close. Probably need to move the clipping out a bit more.

You probably shouldn't be able to activate this from the far side of the closed gate.

There were a few places I saw where lighting was a bit off, with really, really dark shadows--this is probably the most noticeable example. I realize you're fighting with performance and light count, but a bit of simulated (non-shadow-casting) bounce lighting in a few spots would look a lot better. Or maybe this is just a light size/origin and/or entity origin thing in this case? You're pulling the centers on your lights, yes?
Finally, everything up until the ending is fine, but the ending really doesn't work for me at all. It's a shooter and you go through frantically shooting everything until you enter a room with a bunch of enemies and stand in place quietly so they can knock you out?!? Nah. If you want the player to start the next chapter incapacitated, then I'd suggest doing it differently (knocked out by mechanical something, or stuff collapsing on your head, or gas, or...?).
Keep up the good work--this is pretty cool!