As part of her schemes, the Queen of Blades took control of the beloved protoss matriarch Raszagal. Zeratul later rescued the matriarch, but he found her to be irrevocably corrupted. Sorrowfully he took the matriarch's life to spare her from continuing as the plaything of the Queen of Blades. With her mind freed by the deathblow, Raszagal thanked him and named him as leader of the dark templar. Such an honor Zeratul felt unfit to take, his soul too scarred by his experiences.

For the moment he focused on a more immediate concern: contacting any other nearby protoss who had survived the Queen of Blades' treachery. Tracking protoss power signatures to an obscure moon, he hoped to reunite with his comrades and return to Shakuras with them in order to plan for the future. Instead of comrades, however, he found a former agent of the Queen of Blades -- the enigmatic Samir Duran -- engaged in breeding protoss/zerg hybrid creatures. Although Zeratul destroyed the facility, Duran claimed that it was merely one of many. Duran also revealed that he had been known by many names over the millennia and that he was not serving the Queen of Blades, but rather a "far greater power". Deeply troubled by what he had seen, Zeratul went into self-imposed exile with only a handful of followers at his side. He continued to seek answers for what manner of being Duran truly was, and what dark future he was working toward.