Retreat from AiurEdit
The zerg invasion of Aiur left the planet in ruins. Although the Overmind was defeated the Conclave was destroyed and 70% of the population were dead. To survive the Dark Templar Zeratul suggested the protoss leave Aiur for Shakuras, the Dark Templar homeworld, through the Aiur Warp Gate. Judicator Aldaris reluctantly agreed and survivors were ordered to fight their way to the gate within three days.
The evacuation was hard pressed by the zerg and it proved impossible for all to leave before the gate closed. A rearguard including Praetor Fenix, Jim Raynor, and Ladranix were left behind. On Shakuras the immediate concern of the refugees was to prevent the zerg from gaining a foothold near the gate. With the aid of a Dark Templar warband the local zerg presence was reduced and the area secured until the gate deactivated. The refugees began constructing a new home on Shakuras: New Antioch.
The Brood WarEdit
While the Fleet of the Matriarch was off world retrieving Khalis and Uraj, many of the refugees rallied to Aldaris when the judicator discovered Matriarch Raszagal was under the malicious psychic influence of Sarah Kerrigan. The insurgents took up arms and sought to forcibly remove the Matriarch from power.
The returning Fleet of the Matriarch, led to believe the insurgents were motivated chiefly by Khalai prejudices, put down the uprising. Aldaris was killed by Kerrigan and the rebels' true motivation was only revealed later in the Brood War.
With the rift tentatively bridged the refugees aided the unsuccessful defense of Talematros against the Swarm. and took part in the equally unsuccessful attack on Char Aleph at the end of the Brood War.
After the Brood WarEdit
The end of the Brood War did not bring an end to the challenges faced by the protoss. The newly united Khalai and Dark Templar civilization were faced with the difficult task of integrating on Shakuras. One of Hierarch Artanis' major concerns was preventing a return to tribalism as a result of the inability or unwillingness of some protoss to integrate.
Over the course of their stay on Aiur, tensions rose between the Khalai refugees and the native Nerazim, the Nerazim feeling their culture was being gradually eroded by the Khalai. Tensions came to a high when a Nerazim named Taelus seized the Citadel, in hopes of sparking a conflict between the Khalai and Nerazim that would throw the Khalai off of Shakuras. Vorazun and Mohandar diffused the situation before the Hierarchy sent an armed response, though it cost Mohandar his life.
In 2506, Hierarch Artanis launched the Golden Armada to reclaim the Aiur. Many of the Khalai Refugees took part alongside the Nerazim, but during the attack the xel'naga Amon corrupted the Khala, binding the Khalai to his will. Many were able to sever their nerve cords in time, and escaped with Hierarch Artanis aboard the Spear of Adun. Others were bound to Amon's will, and were sent across the sector to exterminate it of all life.
Hierarch Artanis took the loyal Khalai and reclaimed the Keystone, regrouped with the Nerazim and reactivated the Purifiers on Glacius. Loyal Khalai fought alongside him as he tried to find the xel'naga in Ulnar, but the Khalai found them dead. Later, Artanis and the Khalai refugees recruited the Tal'darim and Purifiers aboard Cybros, and moved to reclaim Aiur. The attack was successful, and using the Keystone Amon was thrust from the Khala, saving those under his control. After six years in exile, the Khalai had reclaimed their homeworld.