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In early December, 2499, the magistrate was assigned to help defend Mar Sara and prevent panic. With the recent destruction of the Chau Sara colony by the protoss, the immediate task was to safeguard the colonists and keep their state of panic from escalating further. To this end, the magistrate was given live-fire command and control training, and repulsed minor incursions of zerg on Mar Sara's space platform and Sons of Korhal troops on the surface.
Shortly afterwards the magistrate was contacted by Edmund Duke, commander of Alpha Squadron, and ordered to relocate himself and other core colonists to an evacuation concentration point in the Wasteland. They were joined and escorted en route by Marshal Jim Raynor and the Mar Sara Colonial Militia. In the meantime, Mar Sara's civilian government was practically replaced by Confederate martial law.
The crisis continued to escalate and the relationship between the colonial authorities and the Confederacy deteriorated further when zerg attacked Backwater Station. Despite Duke's assurances, neither the magistrate nor Raynor were convinced that Alpha Squadron would arrive in time to save Backwater. The magistrate authorized the colonial militia to accompany Raynor and mount a rescue. The operation was a success but also resulted in the destruction of a supposedly "vital Confederate installation". The marshal and his men were arrested by the Confederates. The magistrate protested but Duke brusquely refused to reconsider.
With the zerg spreading unchecked and the Confederacy abandoning the planet and the colonists, the only remaining source of aid was the rebel Sons of Korhal. Arcturus Mengsk, the rebel leader, personally contacted the magistrate, and offered to evacuate the colonists. The magistrate accepted and evacuation was a success. As Mengsk had warned, the magistrate was subsequently branded as an outlaw by the Confederacy for dealing with the Sons of Korhal. This was of little concern given the colony was already lost to the zerg. The magistrate was promoted to "Commander" within the rebel group.
The Commander was reunited with Raynor, whom the rebels had freed from the prison ship Merrimack. The Commander supervised a rebel raid on the Jacobs Installation which recovered Confederate data.
For better or worse, the Commander was now part of the Sons of Korhal. The rebels journeyed to Antiga Prime where an anti-Confederate revolt was imminent. Under the Commander's guidance, Lieutenant Sarah Kerrigan and now-Captain Raynor incited the rebellion and repulsed Alpha Squadron's initial attempt to suppress it. The Confederacy laid siege to the colony and trapped the rebels. Months of bitter fighting followed.
The data stolen from Jacobs Installation provided the means to breakout. They contained designs to the psi emitter - a device that lured zerg to isolated locations. A psi-emitter had originally drawn the zerg to Mar Sara. While the Commander engaged and occupied Delta Squadron, Kerrigan infiltrated the Confederate lines and planted a psi emitter in the enemy base. The zerg descended on the planet en masse and the rebels escaped in the ensuing catastrophe.
Fall of the Confederacy
The Sons of Korhal launched their attack on Tarsonis, and once again the Commander took an active part in operations. As the battle progressed, Mengsk's brutal ruthlessness became all too apparent; the rebel leader ordered the use of psi-emitters on the heavily populated planet, and finally abandoned Kerrigan to the zerg at the Battle of New Gettysburg. The latter act finally caused Raynor to abandon the Sons of Korhal; the Commander and Raynor's Rangers joined him. Together they destroyed Tarsonis' Ion Cannon and escaped the planet.