I remember finding a "TCS Tiger's Claw" DooM map on AOL back in the day. I was all excited to try it out... and it turned out to be a big rectangular room (a hangar?) with some Imps in it.
You are correct that an initial pitch for "Alien Commander" became System Shock, but I believe you're thinking of Wing Commander: Hazardous Duty, which was a pitch the team put together in 1997. It would have been a Quake-engine game. I've heard they had multiplayer up and running with humans versus Kilrathi marines internally at Origin. We recently unearthed a video of the demo level: https://www.wcnews.com/news/2013/05/16/hazardous-duty-pitch-revealed
(Alien Commander would have taken place on the wreckage of the Tiger's Claw.)
Could be a pretty decent UDK project. Think Gears of War in the WC universe...