Naganis assumed a diplomatic role after the Brood War, forsaking the path of the warrior that many Templar followed. While he fitted the job well, the lack of physical activity left him in a less potent condition. He could still fight with psionic blades and cast psionic bolts, though not as proficently as he once could.
A few years after the Brood War, an Alliance force uncovered a set of protoss ruins on Dylar IV, ruins that were to be turned over to the protoss. Naganis and an entourage were sent to represent the protoss at the ceremony, in which they would be given the deed to the site. The coming of the zerg disrupted this however and Naganis, along with the Alliance representative Jim Raynor, was forced to fight and flee to safety, an elite Alliance team guarding him.
Naganis survived the experience, thanked those who aided him and returned to his own people.