However, Kun was not receptive to Vodo's help, and at the brink of death accepted the offer of the spirit of Dark Lord of the Sith Freedon Nadd, and as Nadd healed Kun's broken body without sparring the pain, Kun's scream echoed throughout the galaxy, and no one was more hurt, than Master Vodo. Continuing on to Deneba, Vodo and his two students arrived there just in time to help the Jedi defend themselves against battle droids sent by the Krath. Once the battle of Deneba had been won, Vodo and the Jedi returned to Ossus to talk strategy in dealing with the threat of the Krath and the apparent return of the Sith in the form of Vodo's own former student, Exar Kun.

On Ossus, Vodo sat on a council of Jedi Masters to talk about issues pertaining to the war. One such issue presented before Vodo and the council was the proposal by Jedi Knights Cay Qel-Droma and Nomi Sunrider to attempt a rescue mission to retrieve Ulic Qel-Droma who had joined the Krath in an attempt to defeat them from within, but was becoming dangerously close to actually uniting with them. The council approved the mission but warned the two Jedi that Ulic must return with them by his own free will or he might as well not be rescued at all. The mission failed and Ulic formed an alliance with Exar Kun and the Krath.

Six months later, the Jedi were still at war, and one of their own, Ulic Qel-Droma, had become the new leader of the Krath, and to top it all off, Vodo's former student, Exar Kun, had titled himself the new Dark Lord of the Sith. Wishing permission from the Senate that the Jedi could deal with this threat openly and by any means necessary, Vodo traveled to Coruscant with a band of Jedi to meet with the leaders of the Republic.

However, before the meeting took place, Vodo and the Jedi were attacked by the Krath and its forces, led by Ulic Qel-Droma. Leading the counterattack against the forces, Vodo and the Jedi made their way to the Republic War Room and eventually cornered Ulic. Rendering him weaponless, Vodo and the Jedi were able to place Ulic under arrest and end his reign of terror, at least for the moment. During the delay until Ulic's trial, Vodo returned to Dantooine for some meditation and soul searching.