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.
Chapter IV: The Stand
In the wake of the Overmind's defeat, the Zerg proliferate on Auir, though they are largely mindless. Despite protests from Judicator Aldaris, the remaining Protoss emigrate to Shakuras, led by Prelate Zeratul and the previous game's Non-Entity General, newly named Artanis and promoted to Praetor in Tassadar's place. The new Featureless Protagonist does not get an identity until later, but it's Selendis, a female Protoss, and we'll use that for convenience. Despite pressure from the Zerg, they succeed in evacuating the remaining Protoss through Aiur's last remaining Portal Door, helped by the Odd Friendship in Fenix and Jim Raynor, who stay behind to Hold the Line. Barely have the migrants arrived, though, that they detect a Zerg infestation on the planet: the Zerg have seized the Auiran side of the Warp Gate. After Selendis & Co deal with this first infestation, Fenix and Raynor close the Warp Gate from the Aiur side, escaping via their own means.
The Dark Templar Matriarch, Razsagal, tells the threesome of of two special crystals, the Khalis and Uraj crystals, which can be brought to a Xel'Naga Temple on Shakuras and used to clear out the Zerg infestation. Selendis, Zeratul and Aldaris set out to obtain the two crystals, aided by the most unlikely of allies: Sarah Kerrigan, the Queen of Blades. Arriving, she explains that she is currently free of Zerg control, but that with a new Overmind growing on Char—created by Daggoth, a surviving Cerebrate—she hasn't her freedom for long. After earning Razsagal's trust, she departs with the Protoss for their mission.
The Uraj Crystal is found on Braxis, an ice world once colonized by Protoss but currently under occupation by the Terran Dominion. Even worse, the world is about to be beseiged by humans from the United Earth Directorate Expeditionary Fleet, sent from Earth That Was to regain control of the galaxy. Despite opposition from both Mengsk's rank-and-file and Vice Admiral Alexei Stukov, The Number Two of the UED fleet, Selendis's party succeeds at obtaining the Uraj Crystal and set out for the resting place of the other one: Char. Here, Kerrigan seizes control of a small brood, allowing Selendis control of both the Protoss and Zerg war machines at once. Leaving Daggoth's infant Overmind and now-diminished brood to their own troubles, Selendis's forces return to Shakuras with both crystals.
Here, they discover great trouble: Aldaris had staged a rebellion against Razsagal, with many Auir survivors behind him. Raszagal authorizes lethal force against Aldaris, and Selendis, Zeratul and Artanis are able to capture him. Amidst the heated discussion, however, Kerrigan arrives and executes him. In anger, the Protoss demand that she leave, and she agrees: all she really wanted was the ravaging of Daggoth's brood and the destruction of the Cerebrates growing on Shakuras. Once the Crystals wipe them out, she'll be able to seize Shakuras's growing broods for her own purposes. Despite knowing their actions would benefit their enemy, Selendis, Zeratul and Artanis move forward with the Xel'Naga Temple plan, activating it and freeing Shakuras of the Zerg.
Chapter V: The Iron Fist
The player now takes the role of a UED captain, who is placed under direct command of Vice Adm. Stukov and ordered by the force's leader, Admiral Gerard DuGalle, to establish a forward base on Braxis. Stukov and the Non-Entity General make landfall but discover that They Require More Vespene Gas; all the local geysers are already occupied by Dominion refineries. Salvation comes in the form of Lt. Samir Duran, a Ghost in leadership of the Confederate Resistance Forces, and he and Stukov form an Enemy Mine situation (though, as far as the UED is concerned, the rebels have merely been "conscripted"). Duran also aids them in seizing the Dylarian Shipyards, where the UED is able to commandeer a number of Battlecruisers and use them to repel a counter-attack led by Gen. Edmund Duke.
The UEDEF then travels to Tarsonis, which houses the ruins of the Terran Psi-Disruptor. Though Stukov argues for seizing it, DuGalle sides with Duran and mandates that it be destroyed. The UED Captain and Duran fight through four Zerg broods guarding the Psi-Disruptor, but are stopped at the device itself by Ghosts answering to Stukov, who has announced he will destroy it himself. Next, DuGalle moves on Korhal, the center of the Dominion. Mengsk has both a large Battlecruiser fleet and nuclear silos primed at its defense, and DuGalle allows The UED Captain to decide which one to disable, as there is not enough time to stop both. Depending on the Captain's choice, s/he faces a slightly different challenge as the seige descends to Augustgrad, the capitol city. The UED is successful. The Dominion falls, and Arcturus Mengsk's flagship, the Norad III, is intercepted by DuGalle Aleksander; only the unexpected interference of Jim Raynor, aboard his own flagship Hyperion and backed by a Protoss flotilla, allows Mengsk to escape with his life. And even then, that life might not be very long, since the UED track them to Aiur.
The situation on Auir is complicated: Raynor's base is near the decommissioned Warp Gate, with Zerg broods in all directions—Zerg who awaken when the Warp Gate re-opens. The Captain is ordered to deal with the Protoss guarding Raynor, while Stukov, Duran and DuGalle hold the flanks against the Zerg. Ultimately, the Captain succeeds, but Raynor and Mengsk escape to Shakuras in a Drop Ship; the Warp Gate then self-destructs. In addition, Duran shows his trustworthiness by moving his forces out of position under guise of Fake Static, allowing the Zerg access to the UED war machine. Stukov, who has long doubted Duran's loyalty, leaves the fleet to deal with his own issues.
DuGalle tracks Stukov to Braxis, where he has secreted the Psi-Disruptor. DuGalle, feeling betrayed by his oldest friend, authorizes Duran and The Captain to do what needs to be done. Duran infiltrates the Psi-Disruptor complex and shoots Stukov, disappearing shortly thereafter. Stukov, for his Final Speech to DuGalle, declares Duran the real traitor. He advocated against the Psi-Disruptor, reportedly the only weapon that could defeat the Zerg; he allowed the Zerg to attack at a crucial moment, enabling Raynor and Mengsk's escape; and now he has succeeded in turning DuGalle and Stukov against each other. He is either infested by the Zerg or is working on their behalf. As though to underscore Stukov's words, the computer announces that the Psi-Disruptor's reactor has been set to overload, and that Zerg are smashing their way in. Despite stiff resistance, DuGalle and the Captain make it to the reactor in time to save the complex. DuGalle announces his intention to operate the Psi-Disruptor 24/7 and garrison it—though he will not have many troops to spare, as his next mission requires his full attention:
Char. Here, the Psi-Disruptor's signal has already put many of Daggoth's broods into disarray, but three Cerebrates remain. One can make its Sunken Colonies temporarily invincible; one can respawn a "Torrasque" super-Ultralisk at will, and the third is surrounded by infested Command Centers with which it can make "Infested Terran" Suicide Attackers. Despite this opposition, The Captain manages to secure the Overmind, and UED forces subdue it using powerful drugs. This renders them the undisputed masters of the Koprulu Sector.
Chapter VI: The Queen of Blades
The player steps into the shoes (ooze?) of a Cerebrate on Tarsonis, now serving Sarah Kerrigan. She's not in good shape: though she has the help of Samir Duran, indeed infested, the Psi-Disruptor's signal has reached Tarsonis, and she, Duran and the Cerebrate are forced to put down the feral Zerg. Next, she takes her brood to Braxis, where she conferences with Raynor, Fenix and a recently-returned-from-cryo Arcturus Mengsk. He agrees to turn over to her the Dominion's Psi-Emitters in return for her help in retaking Korhal. With the help of said Psi-Emitter, Kerrigan collects many of the feral Zerg roaming Braxis, eventually overwhelming the scanty UED defenses and destroying the Psi-Disruptor once and for all.
After a quick stop at the resource-rich planet of Moria to refill her brood's coffers, Kerrigan moves on Korhal. Despite defensive efforts from the UED, employing their new Slave Broods, Kerrigan's Zerg are successful, dealing yet another blow to the UED's stranglehold on the Koprulu Sector. (Indeed, she notes that, if the small size of the Slave Brood was any indication, the UED are having trouble controlling their new Overmind.) The easy victory also makes it the perfect time to engage in some Chronic Backstabbing Disorder. General Duke is killed in defense of his Emperor, and Fenix's Protoss are wiped out to a man. Jim Raynor, his wroth roused, swears to kill her for her crimes before departing.
Kerrigan, weary of bloodshed for the first time since her transformation, returned her brood to Tarsonis for recuperation. There, the UED descends with its slave broods. However, Duran identifies the locus of UED control, and Kerrigan is able to turn the slave broods against their masters. Newly augmented, Kerrigan sets out for Shakuras. Besieging the capitol of Talematros, Kerrigan is able to devastate the defenses and kidnap Matriarch Razsagal. She spirits the Matriarch to Char, with Zeratul and Artanis in pursuit. There, she reveals her intentions: Zeratul can have his beloved monarch back if he aids her in destroying the new Overmind. Despite his mistrust, he complies; but when he asks Razsagal if she wishes to return to Shakuras, she declines, and Kerrigan "admits" that she took mental control of Razsagal quite a while ago, thus turning the Protoss into perfect tools. Zeratul, incensed, arranges for transport to the surface of Char, where he arranges for a warp transit back to Shakuras. With only 30 minutes to stop him, Kerrigan orders the full might of her broods to descend on Char. She does not succeed in killing Zeratul or Razsagal, however—because Zeratul, realizing his beloved Matriarch is gone forever, slays her himself. Freed from her mind control, Razsagal declares Zeratul the new ruler of the Dark Templar, and Kerrigan lets him leave, knowing he will not be able to live with himself.
Zeratul, attempting to locate Artanis, instead stumbles upon a secret lab where unholy experiments have been taking place: someone is attempting to create Protoss-Zerg Hybrids. That someone is revealed to be Samir Duran, who claims to be thousands of years old and serving some higher power. Zeratul destroys the lab, but its contents will continue to haunt him.
Kerrigan reclines in state on the orbital platforms above Char, but her rest is not easy: Artanis arrives to avenge Fenix, DuGalle arrives to avenge Stukov, and Mengsk arrives because he's a Jerkass. Most of her broods are on the planet surface, with only her loyal Cerebrate in space to defend the platform. Despite desperate odds, and Duran's unexplained absence, she and the Cerebrate repel the invaders. Mengsk is sent home with his tail between his legs, as is Artanis; but the UED, who have been a thorn in her side for so long, receive no quarter. Kerrigan sits now atop the ashes of the Koprulu Sector, the Queen of Blades and self-proclaimed "Queen Bitch of the Universe."