Although the Khala ushered in a new era of peace for the protoss following the Aeon of Strife, not all were willing to embrace the new doctrine. These dissidents, known as the Rogue Tribes, feared the Khala. The rogues held no ill-will toward their brethren and attempted to live their lives unnoticed as best they could. Nonetheless their existence was known to the Conclave.
Approximately one thousand years before the Great War, the Conclave, under the leadership of Kortanul, had collected records on the locations of the Rogues. The list was lengthy and included members of all the tribes. The majority of the Rogues belonged to the Sargas Tribe.
The Conclave ordered the new, young executor of the Templar, Adun, to report by himself to the Conclave's Great Forum, in order to discuss the Rogue Tribes with him. Adun was shocked by Kortanul's description of them; by cutting themselves off from the Khala, they could create a new Aeon of Strife. Adun was given Raszagal, a young prisoner, to question. Adun felt that the slaying of other protoss could also create another Aeon of Strife. He requested permission to bring the prisoner with him to the Citadel of the Executor so the other Templar could question her. The Conclave agreed, but demanded a recording of her execution, quickly. In addition, they gave him their information so he could quietly track down the other rogues, abduct them, and execute them.
Adun was unable to bring himself to execute the Rogues, as his mental linkings with them showed that they were sane and had no intention of harming the other protoss. He transmitted fake recordings of the executions to the Conclave, meanwhile relocating the Rogues to places of safety. However, Adun knew the Conclave would eventually discover his disobedience, so he began teaching the rogues how to cloak themselves from the Conclave. The Rogues ended up developing these abilities more quickly than Adun could teach them.
Unfortunately, the Rogues, still learning their powers, lacked the discipline of the Khala. They inadvertently unleashed psionic storms, which spiraled out of control on Aiur. The Conclave, scattering the storms "at great cost," discovered the corpses of dead Rogues, only to realize these Rogues had been depicted in the execution recordings. Inter-tribal warfare erupted as protoss who refused to follow the Khala were branded as traitors and hunted down. The surface of Aiur was scarred and many warriors were slain in massive engagements. The war reached the Dark Templar's ancestral home, and they defended it from khalai protoss that attempted to remove them.
The Conclave captured the remaining Rogues in secret. However, they could neither punish Adun nor slay the Rogues, as he would force them to publicly admit the existence of the Rogues. The Conclave decided to banish the wayward Rogues from Aiur forever. The Templar under Adun were sworn to silence as the Rogues were loaded onto an ancient, but functional xel'naga ship, along with other ships Adun had insisted travel with them. However, Adun's presence prompted Kortanul to psychically attack the Rogues, who responded in kind. Adun feared the Rogues would accidentally create another psionic storm. He created a blue mist with a combination of Khala and strange energies, which covered and protected the Rogues. However, the power caused Adun to burn out like a star.
"Have I not pledged myself to your cause? Not all beings are as unforgiving as your lamented Conclave, Aldaris."
Inevitably some knowledge survived on Aiur and over time the rogues became the subject of myth and legends. Eventually they became known, in legend, as the Dark Templar.
Over the next thousand years, the Nerazim would be hunted and persecuted by the Khalai. Regarded as heretics by the Khalai, the Conclave decreed that even consorting with "the Fallen Ones" was heresy. However, even with the brutality of the Conclave, under Matriarch Raszagal, the main body of the Nerazim would often aid their Aiur brethren from the shadows, though some groups of Nerazim would engage in retaliation strikes against the Khalai.
The two kindreds were finally reunited during the Brood War, though tensions remained, both during the conflict (where the Khalai and Nerazim even fought one another despite the threat of the zerg), and in the years beyond. Even after the End War and reclamation of Aiur, the wounds between the Khalai and Nerazim remained. Vorazun reasoned that the kin-strife between the Khalai and Nerazim should never be forgotten, but healed over time through empathy. Through learning the lessons of the past, perhaps the protoss could achieve a brighter future. When rogue spectres attacked the Terran Dominion, she was reminded of the Discord, and how the Nerazim had been similarly feared by the Khalai.