The missions are individual battles. Complete each mission, and you are awarded prestige. You can then use your prestige to, earn promotions, get new ships, request new officers, or requisition supplies and ammunition. As your prestige increases, you are given more difficult missions, and so the loop pretty much continues. SFC's graphics aren't top of the line, but they certainly aren't hard to look at.
Space is vast and expansive, and contains all manner of objects.
Asteroids, nebulas, and planets are all rendered beautifully. The ships themselves look very much like the Star Fleet battles miniatures that they were more than likely modeled after, and is always a pleasure to watch them swooping back and forth pitching chemical and mechanical death at each other. In large part, Starfleet Command sounds as good as it looks. I knew I was in for a treat when the game opened, hit me with the paramount logo, and treated me to the enterprise running away from three klingon cruisers in surround sound. Most all the Star Trek effects from the movies are reproduced to exceptional detail.