Plot
The game takes place fifteen years after the original game. After destroying the Taiidan Emperor and reclaiming their ancient homeworld of Hiigara, the Kushan re-establish their clans, or "kiith", in a great council, though some clans have precedence over others. The Mothership, with Fleet Command and the hyperspace core removed from it, remains in orbit over Hiigara as a shipyard. Meanwhile, the Taiidan Empire has collapsed after years of civil war, and a new Taiidani Republic has arisen as an ally of the newly minted Hiigarans, while the Imperialists and their Turanic Raider allies continue to raid both Hiigaran and Republic space.
The campaign begins with the Kuun-Lan, a mining vessel belonging to Kiith Somtaaw (one of the minor clans), launching from the dry dock orbiting the Angel Moon to assist Kiith Nabaal carrier Veer-Rak and its fleet to defend Hiigara against the Imperialists' assault. While aiding a Hiigaran destroyer attacked by Turanic Raiders, they soon find a derelict beacon pod, which the crew decides to capture and research with the aid of the research vessel Clee-San, sent by their clan leaders back on Hiigara, who order that the beacon and its technology be kept within Kiith Somtaaw in order to gain an advantage over the other clans. As they study it aboard the Kuun-Lan, a strange virus begins to take over the ship. The part of the ship containing the derelict is jettisoned; the Clee-San then scans the jettisoned part of the ship to determine what happened. As it scans, the jettisoned portion of the ship fires a beam at the Clee-San that subverts control of the ship and its escorts. Turanic Raiders arrive and are also subverted, forcing the Kuun-Lan to flee.
Further research suggests that the derelict pod carried techno-organic nanobots which they call "the Beast", that can take control of machinery and even people. The Kuun-Lan seeks a Bentusi trading ship for help, and find it being attacked by a Beast fleet. The trading ship is hit with an infection beam and self-destructs to avoid being subverted. While other ships are assimilated by the Beast, the Kuun-Lan discovers that while the true origins of the Beast are unknown, it was first discovered by an alien vessel called the Naggarok, which had come from another galaxy a million years earlier and had picked up the Beast in intergalactic hyperspace. Before the Naggarok was fully assimilated, the drives and communications of the ship were destroyed by the crew, but the ship automatically released a distress beacon - still infected by the Beast - which the Kuun-Lan discovered. As the Kuun-Lan hunts for the Naggarok, they must also contend with the Imperialist Taiidani, who are experimenting with the Beast in an attempt to weaponize it.
After several battles with infected vessels and Imperialist planetary bases, the Kuun-Lan discovers a siege cannon, which has the potential to be an effective weapon against the Beast. The cannon proves ineffective against Beast-controlled vessels as-is (it also overheats after one shot), so the Kuun-Lan begins searching for the Naggarok so they can use a "pure" sample of the Beast to upgrade the cannon. Upon encountering the Naggarok, they find that the Imperialists have allied with the Beast in return for control of half of the galaxy, and are rebuilding the ship's engines. The Beast offers the Kuun-Lan a chance to join them, an offer that is rejected. The Naggarok, fully repaired, then escapes. As the cannon also uses Bentusi technology, the Kuun-Lan searches for the mysterious traders who had supported the Kushan exiles' claim to Hiigara. However, the Bentusi are panicked by the emergence of the Beast, and attempt to flee to another galaxy. The Kuun-Lan and its fleet destroy the Bentusi's slipgate and engage their tradeships, eventually shaming the Bentusi into helping them fight the Beast.
The Somtaaw fleet soon finds the Clee-San and captures it, using it to lure the infected portion of the Kuun-Lan (used by the Beast as a mothership) before the ship's reactor overloads; the Kuun-Lan then destroys the Beast mothership using the newly enhanced siege cannon. They then seek out the Nomad Moon, a Taiidani Republic battle station incorporating a powerful repulsor field; upon their arrival, they find that the station has already been infected by the Beast. The Naggarok, protected by the station's repulsor field, again offers the Kuun-Lan an alliance, an offer that is again refused. Acting on information from the Republic, the Kuun-Lan is able to destroy the Nomad Moon's repulsor field generators using vessels small enough to avoid its sensors, allowing the main fleet to destroy the station itself. The Imperialist Taiidani, seeing that the Beast did not intend to honor its bargain after witnessing the Bentusi appear, abandon the battle, leaving the Naggarok to be destroyed by the Somtaaw fleet.
After the destruction of the Naggarok, the remainder of the Beast-infected ships are destroyed and a vaccine to the infection is discovered, ensuring that the Beast would never return again. Kiith Somtaaw gains great prestige in Hiigaran society, and are honored with the title of "Beastslayers" for their prominent role in the destruction of the Beast.