The story of the single-player campaigns included with Brood War picks up almost directly where the Starcraft missions left off. The death of the Overmind, having just been slain by Tassadar, has thrown the cerebrates into havoc as each of them battles for supremacy, their wills no longer dominated by their dead master. The Protoss, their ranks having been decimated by the war with the Zerg, pack up camp and use the warp gates on Aiur to make their way to Shakuras, the homeworld of the Dark Templar- but when they get there, they find that the Zerg have already begun their invasion.
During one of the battles, the Protoss forces meet up with Kerrigan, who has also been fighting the Zerg. She reveals that when the Overmind perished, she regained her independance and free will, but also informs the Protoss that there are a number of cerebrates attempting to form a new Overmind on the planet Char. If they were to succeed, the Zerg invasion would renew itself as if nothing had happened- and she would lose her own identity. Reluctantly, Zeratul, Artanis, and the Dark Templar Matriarch Rashagal enter into an alliance with the Queen of Blades as they plot to destroy the Zerg forces on Shakuras- the Protoss interested in their own survival, and Kerrigan interested in destroying her enemies that are located onworld. To accomplish these tasks, they must activate an ancient Xel'Naga temple with a pair of long-lost Khaydarin crystals, the Uraj and the Khalis.
After running afoul of the Terran Dominion forces in the path of their task, the searching forces return to Shakuras, crystals in hand, only to discover that Aldaris has staged a coup d'etat and taken control of Shakuras. Both Protoss armies clash, and the battle ends with Aldaris frantically trying to explain that Kerrigan has greater plans than they realize- but as he speaks, Kerrigan cuts him down from behind. Enraged, Zeratul orders her offworld, and Kerrigan is only too happy to comply. Finally, the Protoss forces activate the Xel'Naga temple, weathering a massive attack by the cerebrates, aware as they are of the impending danger, and scour the Dark Templar homeworld of anything not Protoss- an act that leaves their planet shattered.
The Terran campaign begins at the point, with the United Earth Directorate beginning their conquest of the Terran Dominion, in an attempt to bring all of humanity under their fist- and also to attempt to capture the growing Overmind and bring it under their control. Early on in their initial attack, they make contact with Samir Duran, a man who identifies himself as a dissident and joins with their forces as an expert on the native tactics. On their conquest, they discover an abandoned project of the Terran Confederacy, the Psi Disruptor. Whereas the Psi Emitter has the power to draw Zerg forces to its location, the Psi Disruptor negates the psionic command that cerebrates use on their minions. Duran attempts to persuade Admiral DuGalle to destroy it, but the mission is commandeered by Vice Admiral Alexei Stukov, DuGalle's second-hand man.
The Terran fleet then moves to seize control of the Terran Dominion, still under the thumb of Arcturus Mengsk. While the dictator puts up a vicious fight, the Terran forces destroy his forces on Korhal, and almost have him at their mercy- but Raynor and Fenix, finally showing themselves after the battles on Aiur, pull Mengsk's head out of the fire- and just as Admiral DuGalle prepares to give pursuit, there comes word of treachery by his subordinates. Alexei Stukov has commandeered a portion of the fleet and returned to the reconstructed Psi Disruptor. Duran is assigned to dispatch the vice admiral, and does so- and then vanishes, setting the Psi Disruptor to self destruct. Stukov reveals the treachery of Duran with his dying words- small, almost un-noticable flaws that cut the Directorate off from ultimate victory, and only through narrow chance is the Disruptor saved.
Armed with this knowledge and renewed purpose, the UED moves to subdue the Overmind- and eventually succeeds in doing so. The missions end with a cinematic depicting a news release back home, telling the whole civilian population about their victory in the style of a World War II propoganda report.
At this point, the Zerg campaign picks up, with Kerrigan forcibly removing a cerebrate from its bond with the nascent Overmind and impressing it into her control. As the United Earth Directorate begins fine-tuning its control and the Psi Disruptor begins running at full capacity, she has to pull back her forces and regroup with her unlikely allies- Raynor, Fenix, and Mengsk, and the infested Samir Duran, who has been playing the UED all along under her command. Fortunately for her, the Psi Disruptor is the only one of its kind- and with some Psi Emitters provided by Mengsk in exchange for a promise to put him back in control on Korhal, she is able to destroy it and begin to confront the UED with her forces. Their first step is to assault Korhal, and with the assistance of Raynor and Fenix, Kerrigan is able to eliminate the UED presence on Korhal. As soon as their position is secure, though, she turns on her allies and rolls through their ranks, killing both Fenix and General Duke in the ensuing melee.
Both her allies' power bases in shambles, Kerrigan turns her attention towards the UED and their pet Overmind. To begin the attack, Kerrigan captures the Matriarch of the Dark Templar, and uses her as a hostage to insure the assistance of her followers- as always, only the power of the Dark Templar is capable of destroying the Overmind. The mission goes off well, but when Zeratul demands that she be returned, Rashagal numbly refuses to go. The Protoss warrior suspects correctly that she has been placed under Kerrigan's control, and steals her from under Kerrigan's nose while she consolodates her control. Their escape is cut short when the Zerg forces attack before they can warp offworld, though, and the battle ends with Zeratul killing the Matriarch rather than allow her to live as Kerrigan's pawn. Impressed by this gutsy action, Kerrigan allows her pride to take over and permits the Protoss warriors to leave unmolested.
The final mission comes when the combined armies of three forces- the Terran Dominion, the United Earth Directorate, and the Protoss forces led by Artanis come seeking revenge. Despite the sudden disappearance of Duran, the Swarm rises to the occasion and manages to defeat them all. The closing cinematic shows Kerrigan, gloating in her victory- and Admiral DuGalle, sending a bittersweet message to his wife at home, committing suicide aboard his command ship.
When the secret mission is activated, though, we get to see Zeratul in action once more, as his ships search for Artanis and their surviving brethren. They hit upon a set of Protoss signals, and stumble across a genetics laboratory run by none other than Samir Duran. Duran congratulates them for finding his facility, and reveals that he has been using Kerrigan for his own purposes hungrily telling them of the fate of his greatest creation- a living being brought about by the genetic hybridization of both the Protoss and Zerg species. He ends on an ominous note, casually informing the Dark Templar that the Hybrid has been seeded on worlds throughout the sector- and that when they awaken, they will change the universe... forever.