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Scott's years of training gave him the ability to assess a situation at a glance.
When Alpha Squadron was sent to Bhekar Ro to investigate a strange incident, Scott asked the Squadron's commander, General Edmund Duke, to strike back against the "illegal" Dominion and reestablish the Confederacy. However, Duke refused, as he considered the Dominion the "current" legal government.
During the ground battle, Scott was put in charge of a small commando force consisting of marines, firebats and goliaths, intending to investigate the mysteries of the strange structure which had drawn the attention of the protoss and zerg as well. The group was transported in a trio of dropships but only one made it to the temple. Scott took his depleted forces inside, fighting both zerg and protoss in order to reach the artifact's heart. Once there, he and the remnants of his team were attacked by the artifact itself.
He was later expelled, as the artifact had no interest in terrans. He decided to remain on Bhekar Ro, as he was tired of war. He expressed an interest in colonist Octavia Bren.