Seeking to establish a viable counter-measure to the Republic's clone army, the Confederacy of Independent Systems recruited one of the last remaining Morgukai, Bok, using him as the template for a new clone army. Sora Bulq was given control of this operation, with Tol Skorr operating as his lieutenant. In addition to his role as the prime clone, Bok served as the primary training officer for the clones, tutoring the Shadow Army in Morgukai combat styles. To make them even deadlier, Bulq recruited Anzati assassin teachers from Anzat to further train the Morgukai clones in the arts of stealth and assassination. The necessary cloning facilities were constructed in the magma chambers beneath the capital city on Saleucami, also doubling as the training ground and all powered by the geothermal power stations also built into these catacombs. The clones and their instructors were all equipped with Cortosis alloy blades, to allow them to combat Jedi, though the source of these weapons is unknown. According to the assassin trainer Rath Kelkko, the Morgukai clones adapted quickly to the Anzati methods and techniques, though he noted that proper mastery required years of training and practice.
Unfortunately for the Confederacy cause, the Shadow Army was prevented from leaving Saleucami with a prolonged siege by the Galactic Republic, which ended with their destruction.