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Spoiler warning: Plot and/or ending details follow.
The Xel'Naga came to the Milky Way Galaxy from beyond and were a psionically-attuned, highly advanced race. They had reached what they considered the ultimate stage of evolution, the creation and tending of lesser races.
The Xel'Naga's primary intent was purity of form, and to this end they travelled the galaxy, altering many interesting species they had encountered to enhance the species with this purity of form. However, each time they met with failure.
Involvement with the Protoss
The Xel'Naga journeyed to the edge of the galaxy and to the huge engineered world of Aiur. Upon this world they discovered a psionic hunter race which would be known as the Protoss, who displayed amazing strength, speed and resilience. The Xel'Naga took this to be a sign of purity of form. The species also had a unique psionic link. Seeing them as a successful creation, they were named Protoss, meaning "first-born". The Xel'Naga secretly cared for them, and eventually, when they deemed it ready, revealed themselves to them. The site where they first set foot on Aiur was marked by a Temple which they constructed, over a nexus of cosmic energy.
The Protoss united, fascinated by these new "gods", and learned much from them. Eventually, however, splits developed among the tribes as they struggled on decisions of what they should think of themselves, their inventions, and the Xel'Naga. The Xel'Naga had worked to unite them in one organization, but instead the tribes split and distanced themselves from each other. Indeed, the split was so severe it caused the disappearance of the psionic link. The Xel'Naga, knowing that they had pushed their creation too far too fast, set off from the world disappointed at their failure. The Protoss had just developed spaceflight, and many saw this retreat as a betrayal. The Protoss ships attacked, stopping a few Xel'Naga vessels. The majority of the Xel'Naga escaped, however.
The Protoss, left behind, had only themselves to turn upon. This led to a stage of Protoss history called the Aeon of Strife.
Involvement with the Zerg
Seeing the problems caused by a species with purity of form, the Xel'Naga now set out to create a race displaying a purity of essence.
The Xel'Naga settled over an ash-world named Zerus located in the core of the galaxy, and chose the most insignificant lifeform upon the planet, a larval creature known as the Zerg. While having no ability to affect their physical surroundings, the Zerg had just the traits the Xel'Naga were looking for: genetic versatility and psionic sensitivity. They nurtured these creatures, allowing them to affect their surroundings in almost parasitic ways. Eventually, they began infesting the creatures of the planet, turning them into monstrosities. The Zerg spread rapidly across the planet, infesting or slaying every living lifeform on the surface. In addition to this, they would absorb the creature into their gene pool, allowing the Zerg to replicate and then duplicate them, fueling their rapid growth. The Xel'Naga realized their mistake with the Protoss, and instead of revealing themselves created something to speak for them and contain their collected instincts and sentience. The Overmind was created in the Xel'Naga's fashion to watch over the swarm. The Xel'Naga wanted to centralize the intelligence in the Overmind as opposed to the entire species, like they did with the Protoss. The Overmind, however, was plotting to destroy its creators and spread across the galaxy. A surprise attack was launched against the Xel'Naga, wiping out most of the race's Worldships and the greater whole of the Xel'Naga in the first waves. The ancient ones attempted to flee, but since the Zerg had been able to infest a spaceborne creature, capable of living and thriving in space, they were able to overrun the Xel'Naga Worldships with frightening ferocity and swiftness — consuming their knowledge and eventually leading them onto their eternal journey to the Protoss homeworld of Aiur.
The Xel'Naga have left behind many legacies. On a nexus of cosmic energy on Aiur, they built a Temple to mark the spot where they first set foot upon Aiur. They did the same thing on Shakuras, where their marks (such as darkening the planet and a temple capable of destroying Zerg) are more obvious. Finally, there are prophecies relating to the planet Braken, a Protoss world with religious significance.
The prophecies claim that "he who harnesses this world will someday wield great a power, sanctified by the ancient ones". This could be a reference to the Xel'Naga.