The war ended with all sides withdrawing to rebuild the zerg remained in control of previously infested worlds. The reformed Terran Dominion, UED remnants, and protoss attempted, and failed, to oust Kerrigan. Zerg betrayal dissolved the alliances of convenience. Kerrigan manipulated both anti-UED terrans and the protoss to destroy the Psi Disrupter, break UED control over the sector, and slay the Overmind, thus bringing the entire Swarm under her control. The UED used the psi disrupter to fragment opposing zerg. The zerg civil war was complicated by the arrival of the United Earth Directorate Expeditionary Fleet in the Koprulu sector the UED overthrew the Dominion, and captured the second Overmind with the intent of using the zerg to maintain control over the Sector. Kerrigan sought to kill the Overmind before it could mature and resume control over the entire Swarm and her. Daggoth initiated creation of the second Overmind. The Overmind's death left the Swarm divided between the cerebrate Daggoth and Kerrigan. The protoss subsequently withdrew to Shakuras, the Dark Templar homeworld. The Overmind relocated to Aiur, where it was slain by Tassadar. Resistance against the zerg invasion was hampered by the protoss Conclave's overconfidence and a short protoss civil war. Kerrigan remained on Char while the Swarm invaded Aiur. This created a brief mental link between Zeratul and the Overmind, through which the Overmind learned the exact location of Aiur.
Zeratul, wielding the Dark Templar's power of the Void, permanently slew Zasz. The zerg were attacked on Char by the protoss a renegade Tassadar joined forces with Dark Prelate Zeratul on Char. It had no concern over the other races of the galaxy. The Overmind intended Kerrigan to succeed it as the Swarm's leader, freeing the zerg from Amon. The zerg captured Sarah Kerrigan at New Gettysburg and withdrew to Char to transform her into the Queen of Blades. The terran rebel group, the Sons of Korhal, used and manipulated the invasion to overthrow the Terran Confederacy and form the Terran Dominion. Protoss purification, and terran internal strife, failed to contain the invasion. The Great War broke out with the zerg invasion of the terran worlds. The protoss detected the zerg, learned of their xel'naga origins, and dispatched the Koprulu Expeditionary Force under Executor Tassadar to deny the zerg a foothold. The Overmind ordered the assimilation of the terrans their psionic potential was needed to fight the protoss. Having assimilated multiple species and evolved during the journey, the Swarm arrived at the Koprulu sector near the Protoss Empire. However, it was aware of the directive implanted into it by Amon, and sought ways to subvert Amon's plans. Through this, the Overmind became aware of the existence of the protoss, and through them sought to make the Zerg Swarm perfect. Most were slain and their knowledge was assimilated by the swarm. The two factions fought in the space above Zerus, and the swarm was released on the xel'naga. However, the xel'naga in Ulnar caught wind of Amon's plan, and sought to stop Amon from ending the Infinite Cycle. The primal zerg, meanwhile, went into hiding to preserve their individuality.
The Overmind oversaw the zerg swarm's rapid evolution, created the cerebrates, and divided the Swarm into broods. The xel'naga created the Overmind to control the zerg swarm and prevent a repeat of the protoss' Aeon of Strife. At this point the zerg species diverged into two distinct branches the Zerg Swarm that had been altered and the primal zerg that managed to avoid the tampering of Amon's xel'naga. The fallen xel'naga directly intervened in the zerg's development to gift them with the purity of essence, making them the counterparts of the protoss, gifted with the purity of form the zerg and protoss were intended to eventually merge to form a hybrid army for Amon. Amon's xel'naga discovered the original zerg on Zerus.
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