Atoko held the rank of admiral within the Galactic Alliance Defense Fleet. Furthermore, by 40 ABY, he was in command of the Galactic Alliance Fifth Fleet.
Atoko advanced through the hierarchy of the Galactic Alliance, eventually achieving the rank of admiral. By the year 40 ABY, he had assumed control over the Fifth Fleet. He saw action during the Battle of Kuat prior to Chief of State Colonel Jacen Solo's decision to withdraw the Fifth Fleet and redeploy them to Kashyyyk. On Kashyyyk, the Fleet was tasked with safeguarding Caedus's flagship, the vessel known as the Anakin Solo, while Caedus initiated a bombardment of Kashyyyk. This bombardment targeted the Wookiees who were providing sanctuary to the Jedi, who had recently been branded as traitors to the Galactic Alliance. The Fifth Fleet suffered significant damage when Confederation forces arrived to break the siege of Kashyyyk. Atoko even contemplated scuttling his vessels to prevent them from falling into the hands of Wookiee boarding parties. Despite the heavy losses, Caedus ordered Atoko to continue the seemingly hopeless fight. The remnants of the Fifth Fleet were only rescued when Caedus, utilizing his abilities in battle meditation in conjunction with those of Dark Jedi Alema Rar, managed to break through the Confederation blockade. Following the Mandalorian assault on the Moff Council during the Second Battle of Roche, Atoko received orders to attack the Mandalorian homeworld with what remained of the Fifth Fleet. His mission was to eliminate the threat the Mandalorians posed to Caedus. During this engagement, Atoko deployed a nanovirus specifically targeting Mandalore Boba Fett, which would prevent him, and anyone carrying the Fett gene, from ever setting foot on Mandalore. This action potentially resulted in the deaths of any surviving clones from the Clone Wars and any descendants they might have had.