When the Separatist crisis deteriorated into full-scale war, Master Rancisis was called upon once again to utilize his skills in battle as commander of the Republic's forces. When the Separatists launched an attack against the cloning facilities on Kamino, Master Rancisis served as the battle commander for the defense forces. At the Battle of Kamino, Master Rancisis developed the strategy that allowed the Jedi and Republic forces to repel the Separatist attack and save the facilities.

Near the end of the war, Master Rancisis was deployed to Saleucami to lead an assault against the Separatists' own cloning program. Devised by Count Dooku, and overseen by Dark Jedi Sora Bulq, the Separatists built up an army of Morgukai clones and had them trained by Anzati assassins. The Morgukai were an ancient order of Nikto warriors whose training and attitudes regarding honor and discipline closely resembled those of the Jedi Order. However, at the time of the Clone Wars, the Morgukai had been reduced to a sole remaining warrior, Bok, son of Tsyr. However, Sora Bulq's cloning program would see the Morgukai ranks filled once again, and trained by the Anzati, the warriors would represent some of the fiercest fighters in the galaxy.

The Jedi knew that if the Separatist succeeded in unleashing this Morgukai army, their hopes for victory would be lost. In response, the Republic deployed an entire battalion, fleet, and cadre of Jedi to Saleucami in order to stop the Separatists. For five months the Jedi and Republic forces laid siege to Saleucami under the command of Jedi Master Rancisis. While the campaign prevented the Separatists from leaving, the siege quickly turned into a stalemate. The Separatists' cloning facilities lay protected behind and below the walls of a heavily defended city. A city-wide protective shield prevented a ground attack or orbital bombardment from succeeding, and powerful ion cannons prevented the Jedi's air support from taking out the shield batteries.

As Jedi generals Quinlan Vos, Sian Jeisel, Aayla Secura, and K'Kruhk led troops into battle on the ground and in the air. The battles amounted to nothing more than fruitless attacks and counterattacks that did nothing more than drain the resources of both sides. Nonetheless, Jedi Master Oppo Rancisis used the power of Jedi Battle Meditation in an attempt to influence outcome of the battles.