'''''Chapter I: Rebel Yell'''''
The story begins with the player being inaugurated as the new colonial magistrate of Mar Sara (after an optional training mission). The player travels to the Wasteland to meet up with the local Marshal, Jim Raynor. After establishing an encampment, a distress call is received from Backwater Station regarding a Zerg attack. The message is forwarded to Terran Confederacy General Edmund Duke, who assures the player that his Alpha Squadron will handle the matter. Raynor, on the other hand, thinks Duke won't reach the station in time, and mounts an assault against the encroaching Zerg, in the process destroying an infested Terran command center. Duke arrives shortly after to arrest Raynor for destruction of Confederate property. Raynor argues that the command center was unsaveable, but to no avail: Raynor is arrested and the player's tenure as magistrate is suspended.
Shortly after, the player receives a transmission from Arcturus Mengsk, the leader of the rebel faction Sons of Korhal. Warning that the Zerg are growing in strength and that they will shortly overwhelm the Terran presence on Mar Sara, he offers to evacuate the player's forces and free Raynor from prison in exchange for loyalty. The player's forces are safely evacuated, but before they leave the planet, Mengsk asks the player to infiltrate the Jacobs Installation, a Confederate research lab, to retrieve an important data disk. Not long after, the planet is overrun by the Zerg. This attracts the attention of the Protoss Expeditionary Forces, who burn the surface of the planet from orbit, cleansing the Zerg presence, but unfortunately all other sentient life as well.
Mengsk and the player's forces relocate to Antiga Prime, where the population is sympathetic to the Sons of Korhal, but kept in line by General Duke's Alpha Squadron. With the help of Mengsk's right hand officer, Lieutenant Sarah Kerrigan, a telepathic Ghost operative, Raynor and the player assassinate the leader of the Antiga colony, and the population enter into open revolt against the Confederacy. Duke is dispatched to put down the rebellion, but his flaghip, ''Norad II'', is shot down by Zerg flyers. Sensing an opportunity, Mengsk offers to rescue Duke's forces, if he and Alpha Squadron would defect. Duke reluctantly agrees.
At this point, Mengsk reveals what was on the disk from Jacobs Installation: schematics for a device called a Psi-Emitter, which is capable of attracting the Zerg from lightyears away. Mengsk believes that this was what attracted the Zerg to Mar Sara in the first place, and that the Confederacy plans to continue using the Zerg as a weapon. Mengsk plans to use their own weapons against them, by deploying Psi-Emitters amongst Confederate strongholds. The plan works, allowing the Sons of Korhal to escape. Antiga is overrun, and again, the Protoss arrive to cleanse the planet of Zerg.
Mengsk now turns his attention to Tarsonis, the Confederate capitol world. Using General Duke's knowledge of the planet's defenses, the Sons of Korhal dispatch the Delta and Omega squadrons defending the orbital platforms. Another set of Psi-Emitters is deployed. Kerrigan is incensed that Mengsk would continue to use them. At that point, the Protoss arrive, presumably to repeat their performances on Mar Sara and Antiga. this time, Mengsk orders Kerrigan and the rest of the Sons of Korhal to defend the rampaging Zerg from the Protoss. The Protoss are dispatched, but a huge wave of Zerg approach Kerrigan's position. Kerrigan demands evac, but Mengsk ignores her and moves his fleet away from Tarsonis, leaving Kerrigan stranded.
For Raynor, this is the last straw. He announces he's leaving, and taking his forces with him. Mengsk warns Raynor that he will not let anything impede him, and he "will rule this sector, or see it burnt to ashes around him." General Duke has activated Tarsonis' defensive Ion Cannon, but Raynor's forces take it out and quickly leave. Mengsk declares the dissolution of the Confederacy, and in its place, establishes the Terran Dominion, with himself as Emperor.
'''''Chapter II: Overmind'''''
The player's perspective shifts to that of a newly-created Zerg Cerebrate, a being responsible for commanding the Zerg broods. Whereas other Cerebrates are charged with commanding vast swarms of Zerg, the player's purpose is much more focused: it is responsible for guarding a chrysalis, in which the Overmind is growing a great champion for the Swarm. The cerebrate clears out the last Terran resistance on Tarsonis, with the assistance of two other Cerebrates, Daggoth and Zasz. The player then clears a path through the Protoss fleet in orbit. The Swarm leave Tarsonis and travel to the lava planet Char.
The chrysalis is releasing psychic energy that draws the Terran Dominion to Char, requiring the cerebrate to double down on defense. The Dominion are rebuked, and Daggoth continues to pursue them while the player returns to guarding the chrysalis. Then, Raynor's Raiders arrive on Char, but they are too late: the chrysalis hatches, and a fully-infested Sarah Kerrigan emerges. She makes short work of Raynor's encampment, and warns him that she could easily destroy them all, but allows them to leave. Raynor's Raiders pull out of Char.
Kerrigan now wishes to further the psychic powers she had developed as a Ghost. Zasz reminds Kerrigan of the Swarm's ultimate mission, but Kerrigan refuses to be pushed around by any Cerebrate. The Overmind dismisses any worry about Kerrigan's loose cannon status, assuring the other cerebrates that she is completely under his control. With that, the Cerebrate is tasked with sending forces to accompany Kerrigan as she searches the Terran Science Vessel ''Amerigo'' for data on the Ghost project.
Upon returning from the ''Amerigo'', Kerrigan senses that the Protoss have been hiding on Char for some time now. The leader of these protoss, Tassadar, makes contact with Kerrigan. Kerrigan recognizes Tassadar as the leader of the Expeditionary Force that torched Mar Sara and Antiga and nearly cleansed Tarsonis as well. Likewise, Tassadar recognizes Kerrigan from when she was still human, leading the force to eject the Protoss from Tarsonis airspace. Kerrigan taunts Tassadar, suggesting his powers have waned since last they met. Tassadar counters that he need not make a big show of his powers in an infantile display of power. This infuriates Kerrigan, driving her to raze the Protoss encampment on Char. Zasz warns against acting rashly against Tassadar, but again he is ignored. Once the Protoss camp is in ruins, Kerrigan demands that Tassadar show himself. Kerrigan engages Tassadar in one-on-one combat only to discover that she was fighting an illusion.
Suddenly, Daggoth informs Kerrigan that Zasz has been slain, and that the Overmind's usual ability to reanimate the fallen cerebrates has somehow been nullified. As a result, Zasz' Garm Brood has gone berserk, killing everything in sight. Kerrigan is ordered to slay all that remains of Zasz' wayward brood. The Overmind is displeased with this turn of events. However, in the moment when Zasz was slain, the Overmind touched minds with Zasz' assassin, the Dark Templar Zeratul, learning from him the location of the Protoss' homeworld of Aiur. Kerrigan is tasked with trapping and exterminating the Dark Templar, to insure they do not interfere with his plans again.
The Dark Templar seemingly eliminated, the Overmind sets his sights on Aiur. The cerebrate is tasked with procuring a fragment of the Khaydarin crystal and bringing it to the Xel'naga temple on Aiur. Upon completion of this task, the Overmind, previously existing only as mind, is able to manifest itself as a giant, pulsating structure embedded in the crust of the planet. A foothold thus established, the Overmind sends forth the swarm, intent on assimilating the entire Protoss race.
'''''Chapter III: The Fall'''''
The perspective shifts again, this time to the new Protoss Executor, appointed to fill Tassadar's old position after he refused to burn Tarsonis and was exiled for it. Right now, the Zerg are rampaging across Aiur, and the Judicator Aldaris tasks the executor with aiding Praetor Fenix in the defense of Antioch province. Shortly after repelling the Zerg from Antioch, Tassadar returns. From his time spent with the Dark Templar, he's learned that the way to defeat the Zerg is by destroying the Cerebrates that control them. Aldaris accuses Tassadar of heresy for consorting with the Dark Templar, but Fenix thinks he can carry out the task and implores the executor to clear the way for him. Tassadar disappears again, and the way is cleared for Fenix to remove a cerebrate. Unfortunately, shortly after its destruction, it is reanimated.
His distrust in Tassadar seemingly justified, Aldaris turns his attention elsewhere. Fenix is tasked with defending Antioch while the executor is sent to liberate Scion province from the Zerg. In the midst of retaking Scion, Fenix sends out a distress call, as he is being overwhelmed by the Zerg. Ultimately the Zerg are beaten back, but Fenix is killed in the battle.
The Protoss appear to be winning in the battle against the Zerg, and so Aldaris declares that his current priority is to hunt down and arrest Tassadar before his corrupting influence causes any more damage. Tassadar is tracked to an orbital platform over Char, where he has allied himself with the Dark Templar and with Raynor's Raiders. The executor is ordered to arrest Tassadar, but Tassadar implores them to hear him out. Aldaris accuses Tassadar of lying when the attempt to destroy the cerebrates failed, but Tassadar explains that only the Dark Templar are capable of preventing the cerebrates from being resurrected, and implores the executor to help them find Zeratul. The executor joins with Tassadar and Raynor, and head to the surface of Char, believing Zeratul to be hidden within an abandoned Terran installation. They find him and his Dark Templar, and ask for them to return to Aiur. Despite the fact that they will be branded as heretics, they still feel loyalty to Aiur after all this time and agree to return.
Upon returning to Aiur, Tassadar discovers that Fenix has returned from the dead, his body implanted in a robotic Dragoon walker. He warns Tassadar's forces that the Protoss Conclave is coming to take Tassadar into custody. Tassadar and Zeratul's forces begin to fight the conclave, but Tassadar can not bear to see Protoss fighting Protoss, and surrenders. Zeratul and Raynor immediately set out to rescue him as he stands trial. Aldaris accuses Zeratul of heresy, while Zeratul counters that Aldaris' blind devotion to orthodoxy is causing the Protoss more harm than good.
The Dark Templar are now ready to strike at the Zerg. They locate and dispatch two Cerebrates, and then turn their attention to the Overmind itself. Aldaris, seeing that Tassadar was right about the Dark Templar all along, apologizes and wishes the combined forces of Tassadar, Zeratul, and Raynor luck in the coming battle. The battle is fierce, but ultimately results in the Overmind's destruction. Seeing that the Overmind is trying to reform itself, Tassadar sacrifices himself, crashing the Protoss Carrier ''Gantrithor'' into the Overmind's corpse.
The Overmind is no more, but Aiur is still in ruins. And far away, Kerrigan still lives.