The Arrival.
When Celestia first started raising the sun, she gave off a powerful psionic signal. The Empire felt it's presence, but the world was far beyond the reach of their warp gates. So they decided to travel the old fashion way, on a space ship. The trip took a long time, a very long time. By the time it finally arrived in Equestria, the extinction had already come to pass. The robotic exploratory crew in the protoss shuttle quickly began it's work in observing pony culture and behavior. Concluding they were a peaceful race, they built a warp gate that would lead back to the protoss home world of Aiur.
The Ponies sent an expedition through the portal and found a ruined protoss city. The expedition began to study the protoss relics, but had very little success in unlocking it's secrets initially. Eventually a unicorn scholar and powerful mage named Discovery found that protoss technology only responded to magic of a certain type. Discovery spent the coming months practicing the manipulation of protoss technology, and learned how to mimic their psionic abilities using her unicorn magic. Most importantly, she found out how to manipulate the Aiur Warp gate.
At the time, she was the only one who knew how to manipulate protoss technology, but many other powerful unicorns wished to share in her wisdom, and learn how to mimic protoss psionics. In the coming years, she would train others in her techniques, and slowly the unicorns rebuilt the protoss warp network. Still being the only one able to manipulate the warp gate, Discovery sent expeditions through the gate to the last used planets. While one of them lead to a worthless and lonely ice world, and the other lead a world later discovered to be called Tarsonis, the third lead to another ground breaking discovery, the Dark Templar home world of Shakuras. (In Broodwar, the 3rd to last place the gate lead to was Shakuras during the first mission of the protoss campaign. The 2nd to last time was when Rynor used it to escape the UED, sabotaging it before he made his escape. In the Dark Templar saga, it was repaired and used again to escape to an unnamed world where Zerutal was discovered in a brooding state after being forced to kill his matriarch.)
The discovery of Shakuras brought with it the location of the Dark Templars memory crystals on the planet Ehlna. Without authorization, or the support of a funded expedition (as her expedition was on orders to study the recently discovered Shakuras), Discovery proceeded by her self in search of the prized memory crystals. After much searching, she found said crystals and began to take in their knowledge. Inevitably, she activated the crystal holding the still conscious essence of the ancient preserver Zamara. Discovery was placed into a stasis as Zamaras memories joined with hers. After almost a year of processing, Discovery's mind was overwhelmed by the knowledge, and the unicorn named Discovery was no more. Having absorbed the memories of a mind older than Celestia herself, the Unicorn returned to her people under the name Zamara. It was unclear if Zamaras actual consciousness was now inhabiting her body, or if the flood of thousands of lifetimes worth of memories simply buried her old memories. Whatever the reason, the ancient (and possibly last) protoss preserver had returned in the form of a unicorn.
With thousands of lifetimes experience behind her, Zamara was more than qualified to operate and repair the protoss technology. More importantly, she once again unlocked the secrets of the protoss psychic link called the Khala. Astounded by Zamaras collective wisdom, psionic power, and mastery over the protoss technology, many unicorns agreed to join in her link and a new Khala was born. This new breed of unicorn would eventually rename themselves the Khalai, after the Khalai protoss that came before them.
Not only was Zamara growing in psionic and technological prowess, but many of the kingdoms unicorns were slowly starting to join in the new Khalas ranks. Overtime, relations with the Canterlot government and the New Khala would break down.
The severance.
Upon discovering that Zamara was weaponizing the protoss technology, Celestia put a halt on Khala technological advancement. Zamara had no intention of a violent revolt and tried to negotiate a lift on the further study of protoss technology. Celestia however would not be persuaded, and sent an army lead by one of her best officers, Commander Steelwing, to make sure Zamara complied.
While the Khalai Ponies were the only ones who were able to reverse engineer protoss technology, the technology of a "lessor" race was also left behind on Aiur. A race known as the terran left a large military complex behind on Aiur (from the UED invasion of Aiur during the terran campaign of broodwar). This technology was crude and simple enough that any pony, regardless of race or magical talent, could operate it. While Zamara had only recently starting making major advancements in Protoss technology, the other ponies had been making leaps in understanding Terran technology and weapons. Zamara knew open resistance at the moment would be pointless, instead she bid her time.
As no other ponies outside the Khalai were able to use the warp network, the Khalai secretly built a fleet beyond the seeing eyes of Commander Steel Wing. In time, the "Golden Armada" was deemed powerful enough to successfully defend Aiur. While their numbers had grown, they were still as nothing compared to Commander Steel Wings numbers, and didn't have the man power to properly man their ships. In order to raise their ranks, they used the protoss robotics technology, and with it, they had a fleet they were sure could stand up to Celestias puppet; Commander Steel Wing.
With everything in place, Zamara made her move. Still unaware of Zamaras amassed fleet, the ponies of Equestria were very lax about security. They'd never had a single incident on the home front. Using their enemies complacency to their advantage, Khalai commandos crossed over to Equestria, and sabotaged the gate. The Ponies of the Koprulu sector were effectively cut off from all of Equestria.
Knowing Commander Steel Wing would retaliate, Zamara ordered a pre-emptive strike against Steel Wings Fleet. Steel Wing was caught off guard as the Golden Armada warped in from seemingly nowhere and broke his blockade over Aiur. Taking advantage of the element of surprise, the Khalai used the protoss warp network to quickly capture as many of Steelwings colonies as possible. A short and bitter war would later ensue as Commander Steel Wing readied his fleet for retaliation. Steel Wing knew Aiurs weakness. While he had no idea how they managed to man a fleet so large, he knew the Khalai still didn't have enough man power to fight his forces on the ground and space at the same time. Still having the larger fleet, despite the initial losses, Steel Wing lead a campaign, recapturing one world after another while slowing chipping away at the Golden Armada. Victory was close for the Commander, but Zamara expected this.
The Khalai weren't the only ones upset by Celestias grip on the Koprulu sector. Seeing that they were no longer living under the fear of Celestias immense power, a number of fleets and colonies deserted Steels Wings campaign declaring independence. With his numbers so heavily reduced, Steel Wing knew victory against the Golden Armada was out of reach. Zamara offered a cease fire, and Commander Steel Wing reluctantly accepted. This short war, known as the Khalai Rebellion, was the first major conflict to beset the Koprulu sector since the ponies had arrived. It would be the first of many.