After the initial battle, Naiko continued to play his role as a general for the Rogue's along with Namla throughout the entire Great Sith Civil War. However, he and Namla did not get along with each other at all and the two would consistently fight. At one point, the two drew their weapons at each other but under Darth Exitium's order's they could not actually kill each other. Preferring not to disobey his order's, they both reluctantly stood down.