The game begins with the commissioning of a new Mothership, the "Pride of Hiigara", at the Great Derelict at Tanis. The "Pride of Hiigara" is 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 to rally the Hiigaran fleet. Makaan's fleet lays siege to Hiigara, and the Warlord offers a deal to the Hiigarans: if they surrender the Second Core to him, he will spare their Homeworld.