Plot
Homeworld 2 continues the struggle of the Hiigarans and their leader Karan S'jet. While in the original game the player could select either the Kushan or Taiidan races, in the sequel the Kushan are established as the canonical protagonists.
During the events of the original game, the Kushan race of the planet Kharak began a quest to discover and reclaim their home planet. The Kushan discovered the wreckage of the Khar-Toba, an interstellar transport, in a desert on Kharak, and inside found a galactic map etched on a piece of stone. From this the Kushan concluded they had been transplanted to Kharak some time ago. To reclaim their home planet—"Hiigara"— the Kushan built an enormous self-sufficient Mothership to carry 600,000 people on a crusade to reclaim Hiigara. This led to the engagement and eventual defeat of the Taiidan Empire which exiled them.
The story continues that, while it wasn't known at the time, the Hyperspace Core found in the Khar-Toba that was used to power the Mothership was incredibly rare and one of only three in the galaxy. The Cores, of which the Kushan had the second, were left behind by a so-called Progenitor race, which eventually allowed hyperspace travel. The First Core was possessed by the Bentusi: a powerful and enigmatic race of traders who assisted the Exiles during the first game. The third was lost until approximately one hundred years after the Exiles reclaimed Hiigara, found by a Vaygr Warlord named Makaan, who used it to conquer much of the galaxy and—as of the beginning of Homeworld 2—began attempts to capture Hiigara. The story states that religious beings of the galaxy consider the discovery of the Third Core to announce the End Times, during which Sajuuk, thought to be an immensely powerful being, will return. Makaan believes himself to be the Sajuuk-Khar, a messianic figure that will unite the Three Cores and herald the return of Sajuuk.
The game begins with the commissioning of a new Mothership, the Pride of Hiigara, similar in shape and design to the original Mothership and commanded by Karan S'jet, as in the original game. The ship is attacked by the Vaygr during the final stages of construction but escapes. The Bentusi inform the Hiigarans that they must find Balcora Gate, left behind by the Progenitors, behind which is something essential for stopping either the Vaygr threat, the End Times, or both. The Great Harbor Ship of Bentus, last of the Bentusi, sacrifices itself after being ambushed in a Vaygr attack, leaving its Core for the Hiigarans to claim in order to stop Makaan. But the Warlord learns of the Balcora Gate as well, and the game's penultimate mission takes place on the other side of Balcora Gate, where Hiigarans and Vaygr alike discover that Sajuuk is in fact a Mothership-sized Progenitor starship, with sockets for the Three Hyperspace Cores. The Hiigaran fleet engages Makaan's forces and destroys them, claiming the Third Core from Makaan's destroyed Flagship. With all three Cores, the Hiigarans reactivate Sajuuk, abandoning the Pride of Hiigara, and use it to defeat the leaderless-but-still-dangerous Vaygr invasion; Sajuuk is later found to be the key to a galaxy-wide network of hyperspace gates, ushering in a new age of trade and prosperity for all civilized races in the galaxy - the Age of Karan S'jet, the true Sajuuk-Khar.
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