The Dark Templar Caste is the dirty little secret of Protoss Conclave. At the end of Aeon of Strife, when most of the Protoss were embracing the Khala, some tribes did not want to lose their individuality or put their future in the hands of the Conclave. These tribes did not want to continue the fighting and most of them were peaceful and honorable, but they simply did not wish to take part in the Khala. While Khas had no problem with these tribes, future Conclaves viewed any dissent from the Khala as sacrilegious and they isolated the tribes from the rest of the population. Over several centuries, these Protoss became collectively known as the Lost Tribes.
During their isolation, the Lost Tribes discovered the secret of magic and over the course of centuries, learned to master the unfamiliar energy. In the process of learning magic, the Lost Tribes lost most of their psionic powers and became infused with magical energy. Unsurprisingly, the Conclave was terrified by the strange energies under the control of the Lost Tribes and began calling the Lost Tribes that studied magic the Dark Templar.
In order to defeat the growing power of the Dark Templar, the Conclave formed a great army led by the legendary High Templar Adun. Adun's mission was simple: destroy the Lost Tribes. Adun carried out his mission with amazing success and the relatively defenseless tribes were unprepared for the ferocity of Adun's assault. Tribe after tribe fell before the wrath of Adun's army, but once all of the Lost Tribes had gathered at the final stronghold of the Dark Templar, Adun began having second thoughts about his mission. Adun met with the leaders of the Lost Tribes and the Dark Templar and decided to go against his orders and spared their lives. For many years, Adun actively protected the Lost Tribes from any other army sent by the Conclave. The stalemate between Adun and the Conclave may have gone on for decades, but the Dark Templar proved to be their own worst enemy when they conducted a magical experiment that went terribly wrong.
The experiment was supposed to condense the power of a large number of Khaydarin Crystals to create a single powerful crystal, but the designers of the experiment had not anticipated the incredible release of energy that would be caused by the experiment. To make matters worse, the experiment did not directly damage the Lost Tribes at all; instead, the magical energy manifested itself in many nearby cities, killing hundreds of thousands of innocent Protoss. The public outcry against the Lost Tribes was quick and savage and not even Adun could stop the Conclave from forcing the Lost Tribes and the Dark Templar to board one of the remaining Xel'Naga spaceships and exiling them from Aiur forever.
In space, the Lost Tribes became completely dominated by the magical students of the Dark Templar, and all became masters of magical energy at the expense of their psychic powers. Strangely enough, most of the Dark Templar do not blame the Protoss on Aiur for exiling them, although they do have strong feelings against the arrogant, terrified, and controlling Conclave. Most of the members of the Lost Tribes would like to return to Aiur and they continued to do what they could to help from afar. The Dark Templar eventually settled on the planet Shakuras, which orbited a dark star that emitted heat, but no light. On Shakuras, the Dark Templar rebuilt must of what they had lost when they abandoned Aiur and the mysterious Xel'Naga artifacts spread across Shakuras continued to interest the Dark Templar for centuries after their arrival.
The Dark Templar continued to focus on their magical studies and building a thriving society on Shakuras and it was only the arrival of the Overmind on Char that the Dark Templar became actively involved in the affairs of the other Protoss. On Aiur, the Dark Templar leader Zeratul met Executor Tassadar and the two became close allies in their battles against the Zerg. It was through Tassadar's study of Zeratul's magic, that Tassadar was eventually able to defeat and destroy the Overmind. Following the death of the Overmind, the Dark Templar allowed a large portion of the Protoss population to migrate to Shakuras, but the Zerg followed and strife between the two groups of Protoss eventually boiled over into a short, but vicious civil war.