The story takes place four years after the events in Brood War. Emperor Mengsk rebuilt his empire a built a military force while opposing the Zerg force. The game features as its main character a Nova, a Terran ghost, that works for the Terran Dominion's Nova Squadron. She starts off as a Terran officer, working under colonel Hauler in his Ghost squad.
The Dominion has not heard from Kerrigan in years, but they are well aware of their power. The Zerg's peacefulness seem to trouble the Terran force. Mengsk and General Warfield, his advisor, have begun Shadow Blade, a project that uses Protoss technology. By using terrazine gas, they can increase the Terran Ghosts' psychic strength. These new creatures called Spectres follow the will of their true master.
Mengsk is opposed by the Koprulu Liberation Front, that wants to end his reign over the Dominion. This is where Nova comes into the scene. She is set to uncover the mistery behind Project Shadoe Blade, that will involve her in the war between the Dominion and the rebels. With his army consisting of robots and supported by Protoss technology, Mengsk succeeds in taking over the rest of the Terran worlds. Kerrigan continues with her troops and attacks Char but has not struck against the Terrans or Protoss as of yet.