With the help of his officers Lieutenant Sarah Kerrigan and Commander Jim Raynor, Mengsk was able to uncover a secret Confederate plot to draw the Zerg from deep space to wipe out their enemies. He established a secret staging area on the border colony planet of Antiga Prime, and helped liberate the Antigan people from the Confederacy. Soon he was able to recruit Edmund Duke, a former Confederate general, for his own use. Fighting fire with fire, Mengsk ordered Kerrigan to plant a Transplanar Psionic Waveform Emitter secretly within a Confederate base on Antiga Prime. The Zerg were drawn to the planet, and the Protoss fleet, under the command of Tassadar, came once again to incinerate the planet. In his final campaign to defeat the Confederacy, he used the power of the Psi Emitters once again on the capitol world of Tarsonis. Billions of Zerg overran the Confederacy and proceeded to lay waste to Tarsonis’ major cities and industrial centers. Soon the Protoss arrived to “purify” Tarsonis as they had the previous infested planets. Mengsk ordered Kerrigan to engage the Protoss, and she successfully complied. However, a wave of Zerg advanced on her position and instead of sending an evac, Mengsk chose to apathetically abandon his second in command. With the Confederacy now neutralized, Mengsk established his new Terran Dominion, a government just as oppressive as its predecessor, on his home planet of Korhal.

Having crowned himself Emperor of the Dominion, all of the Terran colonies within the Koprulu sector were united under one sovereign rule for the first time. With General Edmund Duke by his side, Mengsk was unopposed by any of the major Terran Militias within the Sector. Having reinforced the armies of the Dominion by forcefully conscripting the remaining warriors of the defunct Terran Confederacy, Mengsk set out to fortify the various worlds under his care. As the final battle concluded on Aiur and the Zerg reeled in disarray throughout the Sector, Mengsk was left to wonder what ever became of his former Lieutenant, Sarah Kerrigan, the self-styled Queen of Blades. The United Earth Directorate arrived a few years later to overthrow Emperor Mengsk I and establish their own Terran empire in the Koprulu sector. They were able to invade the capitol city of Augustgrad, Korhal. However, Raynor retrieved Mengsk on behalf of Kerrigan seconds before his capture. Kerrigan needed Mengsk for his Psi Emitters and promised him the reclaimation of Korhal in return. She was lying of course and never fulfilled her end of the deal. To get his revenge, Mengsk participate in the three pronged final attack against Kerrigan along with the Protoss and UED. Kerrigan succeeded in defeating all three and with his rag-tag fleet beaten and crippled, Arcturus Mengsk fled back to Korhal to lick his wounds and plan the reconstruction of his Terran Dominion.