Wing Commander: Prophecy was the last direct sequel in the Wing Commander franchise. It is a sci-fi combat flight simulator that took many new directions in its design and story, compared to the previous games in the series.

Just some of the new innovations were a new main character (Lance Casey instead of Christopher Blair, who was the main character in the previous three games), a new enemy (Nephilim), and a new game engine (VISION), amongst other changes.