As mentioned before,
Starfleet Command III has made some huge changes. Foremost, the setting has been altered from classic Star Trek to the Next Generation, which in turn alters the ships, weapons, and races involved in the gameplay. In previous games, there were numerous life forms. With the new Next Generation setting, factions have been lowered to the four most notable races - the Federation, Klingons, Romulans, and Borg.
While fewer races seems limiting at first, in reality it allows for a much tighter storyline which leads to less confusion throughout campaigns and missions. The linear plot, which ties together the campaigns, has you playing as each race, first the Klingons, then the Romulans, and finally the Federation. The Borg do not have a story-based campaign. In the main plot, the Klingons and Federation are preparing to construct a joint space station called Unity. The Romulans do not believe in the Klingon/Federation alliance and plan to debunk the space station and infiltrate the alliance.
Throughout the campaigns you will encounter numerous missions that unfold the action of the game. These missions range from small travel jobs to huge war-like situations. Big changes were made in Starfleet Command III in the tactics of missions and the campaigns. Everything seems streamlined from previous Starfleet Command games. Less weapon types to manage, simplified power management and easier control of shields and warp settings.
Aside from the main campaigns, you can play as any race, including the Borg, in the multiplayer and conquest campaigns. These campaigns are open-ended and have no plot to follow. Winning consists of simply gaining control of the entire galaxy. Also available is an online campaign, called Dynaverse 3. The Dynaverse lets you group with players in fleets to take over other players' territories. After a certain period of time, a winner is declared.
