It should do this by default. Try checking file integrity, signing up from the rank & medals screen, and moving around (but watch out for those Klingons!)

Old thread, but since nobody seems to have noticed this I think it's worth posting.

I own the original Gold version of the game, and ran into the same problem. I looked through the game files and that's where I realized some of the files for the Hydran campaign are missing. Missions 1 to 5 are there, as are 9 and 10, but 6 to 8 are conspicuously absent. This might have something to do with the fact the game originally shipped without any special missions for the Hydran campaign (just generic ones) and these were added later. It looks like they were not added properly or were incomplete, and it doesn't look like GOG fixed this (the script files for the missing missions are available, but looking through them they do seem incomplete and so would require some work to get them running).

I looked through Google and any Starfleet Command resource sites I know and unfortunately it doesn't look like anyone ever fixed this.

I had this game on a CD, still do somewhere, and years ago the game once started behaving so as it wouldn't end. It would go through the story line, and I remember this specifically with the Hydran campaign, then all of a sudden it would be a nearly endless starbase assault or starbase defense loop and the campaign would end (sometimes it wouldn't, the loop would continue)