The story continues from where StarCraft left off: Tassadar has killed the Overmind with the price of his life, Aiur, the Protoss home, has been destroyed by the Zergs and Kerrigan has joined the Zergs.
Episode IV – after Tassadar slays the Overmind, the Zerg becomes more and more numerous, but disorganized. Only the some Protoss forces led by Jim Raynor while the rest take refuge in Shakuras, the homeworld of the Dark Templar. The Protoss are followed by the Zergs, the two joining forces, after Sarah Kerrigan explains that the Overmind has no longer control over her. A new Overmind is growing on Char and she needs help to destroy it. The Protoss ask in return two crystals that will help them defeat the Zerg on Shakuras. They soon discovered the pieces needed and slow the Overmind from developing.
Episode V – This episodes features the Terran campaign, where the player joins the United Earth Directorate (UED) Expeditionary Fleet, will have to take over Terran worlds in this area, but these actions make some Zerg and Protoss groups enemies. Mengsk's Dominion is the first fallen enemy but Raynor rescues Mengsk before UED captures him. The two escape to Aiur, where the Protoss are still engaged in a war against the Zergs.
Episode VI – The UED fleet took control of the Zergs and Kerrigan feels the danger of this shift of power. Kerrigan and her new ally Samir Duran gained the support of the Terran forces commanded by Mengsk and Protoss forces from Aiur commanded by Raynor. This alliance takes over Korhal from the UED but after the victory Kerrigan turns on her allies and kills them one by one. Kerrigan then arrives to Shakuras, the home of the Dark Templars and capture their matriarch. With this advantage, Kerrigan convinces Zeratul and kill the Overmind. Kerrigan now controls the Zerg and eventually defeats the Protoss and the UED, becoming the main power of the Koprulu Sector.