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The game continues on the story from Descent/Conflict: FreeSpace, once again thrusting the player into the role of a pilot fighting against the mysterious aliens, the Shivans. While defending the human race and its alien Vasudan allies, the player also gets involved in putting down a rebellion. The game features large numbers of fighters alongside gigantic capital ships in a battlefield fraught with beams, shells and missiles in detailed star systems and nebulae. Free multiplayer games were available via Parallax Online which also ranked players by their statistics. A persistent galaxy was also available as SquadWar for players to fight with each other over territories.

In 2002, Volition released the source code for the game engine to the public. This code became the core of the FreeSpace 2 Source Code Project