The Movie is split into three Segment.
In the first segment of the Movie, John Hawkins and Jim Raynor are attempting to control the colony of Mar Sara in the wake of the Protoss attack on other Terran worlds. After the Confederacy arrests Raynor for destroying Confederate property, despite the fact that it had been infested by the Zerg, John Hawkins joins Arcturus Mengsk and the Sons of Korhal. Mengsk then begins to use Confederate technology captured on Mar Sara to lure the Zerg to Confederate installations and further his own goals. After forcing Confederate general Edmund Duke to join him, Mengsk sacrifices his own second-in-command, Sarah Kerrigan, to ensure the destruction of the Confederacy by luring the Zerg to the Confederate capital Tarsonis. Raynor is outraged by Mengsk's true aims of obtaining power at any cost and deserts, taking with him a small army of the former colonial militia of Mar Sara. Mengsk reorganises what remains of the Terran population into the Terran Dominion, crowning himself as emperor.
The second Segement reveals that Kerrigan was not killed by the Zerg, but rather is captured and infested in an effort to incorporate her psionic traits into the Zerg gene pool. She emerges with far more psionic powers and physical strength, her DNA completely altered. Meanwhile, the Protoss commander Tassadar discovers that the Zerg's cerebrates cannot be killed by conventional means, but that they can be harmed by the powers wielded by the heretical dark templar. Tassadar allies himself with the dark templar prelate Zeratul, who assassinates one of the Zerg's cerebrates in their hive clusters on Char. The cerebrate's death results in its forces running amok through the Zerg hives, but briefly links the minds of Zeratul and the Zerg Overmind, allowing the Overmind to learn the location of the Protoss homeworld Aiur, which it has been seeking for millennia. The Zerg promptly invade and despite heavy Protoss resistance, the Overmind is able to embed itself into the crust of the planet.
The final Segment of the Movie sees Aldaris and the Protoss government branding Tassadar a traitor and a heretic for conspiring with the dark templar. Indaris (The Main character of the segment) initially serves Aldaris in defending Aiur from the Zerg invasion, but while on a mission to arrest Tassadar, Indaris joins him instead. A Protoss civil war erupts, pitting Tassadar, Zeratul, and their allies against the Protoss establishment. The dark templar prove their worth when they use their energies to slay two more of the Zerg cerebrates on Aiur, and the Conclave reconciles with them. Aided by Raynor's forces—who sided with Tassadar back on Char—the Protoss break through the Overmind's weakened defenses and destroy the Overmind's outer shell, but take heavy casualties in the process. Tassadar channels his own psionic energies in combination with those of the dark templar through the hull of his command ship and crashes it into the Overmind, sacrificing himself in order to destroy
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