You played a solider and could walk around a ship, and one of your colleagues was kinda like Q from James bond, he would give you upgrades and stuff. The tech guy reminded me of the dude from the original Deus Ex
One of the missions is that you landed on a planet and it was like a forest/wooded area and had to complete a mission, and at the end of the mission, you had to wait for your ship to pick you up, and you were getting attacked by bad guys.
I never got a chance to beat MDK 2. i had it but lost the game disc. good thing the HD Remaster is on Steam. this game definitely was so awesome back then.
Unreal II: The Awakening? Sounds pretty similar to what you are describing from what I remember. It came out in like 03 or 04 though, so maybe not old enough.