Conflict: Freespace – Silent Threat

Its expansion, Silent Threat, which comprised additional missions, was also released in 1998.

The expansion Silent Threat continues the story in a straight-forward manner. The player joins the Galactic Terran Intelligence (GTI) while the Terran-Vasudan alliance is in a fragile state, and is told to preserve the alliance by ruthlessly pacifying rebellious elements and fending off remnants of the Shivan forces. However, it all turns out to be a cover-up, as the GTI is plotting a coup, and has constructed a Terran-Shivan hybrid superdestroyer of their own, the GTD Hades, which the player must destroy.

Source: Wikipedia, "Descent: FreeSpace – The Great War", available under the CC-BY-SA License.