Federation HQ looks back at Wing Commander Privateer. A little snippet from the very positive article:
However, the game did have a linear mission-based story built-in. In bars you would be able to pick up clues and get special assignments that were related to the story line and which tied in to the mysterious alien ship that was briefly visible in the Privateer intro sequence.
It really makes you want to fire up the game. You can check it out here.