The Fall of Aiur was a pivotal event in the history of the protoss and the war between the protoss and the zerg. The Fall of Aiur began with the zerg invasion of Aiur, and occurred simultaneously with the Protoss Civil War. The war ended when high templar and former executor Tassadar destroyed the Overmind. Unfortunately for the Protoss the damage had already been done and the Zerg, even without the Overmind had claimed too much of Aiur and slew seventy percent of the protoss population. The Protoss were forced to abandon Aiur. The Zerg, despite the loss of the Overmind and many cerebrates, were victorious.
The conflict started soon after the protoss discovered the presence of zerg near terran colonies. The protoss opened the conflict by sending an expeditionary force to destroy the zerg infestation of Chau Sara.
The preliminary conflict failed, however, as the protoss were unable to save the heavily populated terran planet Tarsonis from a massive zerg invasion. Executor Tassadar was ordered to return to Aiur, but instead traveled to Char, the zerg base of operations, following a psychic beacon. While there he came into contact with an outcast protoss sect, the Dark Templar. Together they learned how to defeat the zerg, but the Overmind learned the location of Aiur from them. Tassadar's force was stranded on Char, unable to prevent the zerg invasion. While there the two groups of protoss allied with a band of terrans, Raynor's Raiders.
The Zerg Invasion
The Overmind and the majority of the Swarm descended upon Aiur. One of the Swarm's first tasks was to acquire a khaydarin crystal, which was defended by the Vanguard of Aiur. The Vanguard was defeated and the crystal claimed. The zerg then destroyed an ancient temple which marked the spot where the xel'naga first set foot on Aiur and put the crystal in its place, defeating another Vanguard force to do so. This enabled the Overmind to crash-land on Aiur and remain there in a physical form.
The Protoss Response
The Conclave felt it was winning the war, and sent an expedition to arrest Tassadar over his relationship with the exiled Dark Templar, believing them to be more dangerous than the zerg. Instead, Tassadar took command of these troops and used them to rescue Dark Prelate Zeratul from the zerg.
The Protoss Civil War
Striking the Head of the Zerg
Tassadar's forces created a plan to weaken the Zerg Swarm. They intended on having Zeratul slay two cerebrates commanding broods near the Overmind's locations. Their deaths would distract the Overmind and thin the numbers of zerg between themselves and the Overmind. The plan was successful. Along with Raynor's Raiders, the protoss launched a final assault on the zerg. Tassadar sacrificed himself in order to destroy the Overmind.
Zeratul convinced Judicator Aldaris that the Khalai refugees should retreat to the last functional warp gate on Aiur and flee through it to Shakuras. Zeratul personally led troops to and through the gate, but hundreds of thousands of protoss were killed during the evacuation. Fenix and Commander Jim Raynor volunteered to guard the Aiur side of the gate from the zerg. Large numbers of protoss fled over the course of three days, until Fenix and Raynor were forced to close the gate to prevent more zerg from forcing their way through it to Shakuras.
The remaining protoss who were stranded on Aiur scattered in a panic. One group, led by Fenix and Raynor, remained near a warp gate. They were eventually hard hit by the invading United Earth Directorate.
During the Fall, high templar Erekul summoned motherships from the edge of space known to the protoss. The fleet assembled after the evacuation, but made efforts to rescue stranded protoss. They were unable to discover the location of those who fled, but made an effort to locate them.
The protoss settlers of Shakuras launched at least two return expeditions to Aiur. One such mission, led by high templar Rihod, former high templar Lekila (who had been cut off from the Khala) and a Dark Templar ship commander searched the Velari Templar School for the powerful Kassia crystal. The group took a long time retrieving the crystal, putting them and their ship under siege by the zerg. Lekila and Rihod fused into a twilight archon, transporting the crystal to the protoss ship.
One group of survivors, which called itself the Shel'na Kryhas ("Those Who Endure"), led by the templar Ladranix, coalesced and sheltered in the ruined cities in Antioch. One of their first tasks was to destroy all flying zerg minions, a task made easier by disarray amongst the zerg, which included a lack of spawning.
Protoss military leaders Zeratul, Artanis and Selendis led an expedition to rescue three wounded heroes from stasis cells. They fought the local zerg in order to clear a way to the cells, but a group of Dark Templar, led by Ulrezaj, attacked, killing two of the heroes before surrendering to the protoss forces. During the battle, Zeratul and the others became aware of the Shel'na Kryhas but, believing attempts to rescue them to be futile, kept knowledge of them secret.
The Shel'na Kryhas eventually lost many members to a splinter group, called the Tal'darim ("The Forged"), led by Felanis. The Tal'darim took shelter in the caverns beneath Aiur which had been forbidden thousands of years ago by the Conclave. There they worshiped a mysterious "Benefactor" they called the "Xava'tor". They were controlled by a drug known as Sundrop. The Tal'darim learned to capture zerg, and seemed to suffer fewer losses to the zerg than the Shel'na Kryhas, leading many former Shel'na Kryhas to defect to the Tal'darim.
A trio of travelers approached Aiur, seeking an artifact for reasons which were mysterious to two of them. They were Jake Ramsey, a terran archaeologist and Rosemary Dahl, a former mercenary and assassin, fleeing from the Terran Dominion's Heir Apparent, Valerian Mengsk. Ramsey contained within his brain the spirit of the protoss preserver Zamara, who held a dark secret she desperately wished to bring to her people.
The group were surprised by the large numbers of zerg present on the world, but were rescued by the Shel'na Kryhas. The two groups joined forces.
Zamara needed to acquire the artifact to rescue Ramsey from the tumor her presence was forming in his brain. She did not immediately inform Ramsey of this, however. She arranged for Dahl to sneak into the Tal'darim caverns and see what the defenses were, but she was captured by Felanis and his former templar henchman, Alzadar. They subjected her to Sundrop, which was addictive to terrans as well as protoss. Dahl was eventually reunited with Ramsey and Zamara, and eventually they were able to break her addiction. From her subconscious, they discovered much of the truth behind the Tal'darim — they were, in fact, being controlled by the powerful dark archon Ulrezaj.
The group captured Alzadar and convinced him to work with them. The fugitives, Alzadar and a Shel'na Kryhas force stealthily entered the caverns, acquiring the artifact and avoiding more dark secrets. However, they were discovered and intercepted by the Tal'darim. They discovered that the size of the Tal'darim band had shrunk even faster than the Shel'na Kryhas, as Ulrezaj was sacrificing them for unknown purposes. Furthermore, Felanis was well aware of this, and he even revealed that Ulrezaj served another being. Alzadar and half the Shel'na Kryhas force remained behind to battle the Tal'darim while the rest attempted to flee ... only to be intercepted by a well-led, disciplined zerg force led by an advanced infested terran, Ethan Stewart. This ambush was spoiled by the arrival of a small Terran Dominion fleet, which had been dispatched by Valerian Mengsk in order to pick up Ramsey.
Ramsey, Dahl and the protoss had their own plans. They needed to get to the warp gate, and so they hijacked the Dominion dropship which had picked them up and fled towards the gate in it. The Dominion and zerg forces pursued them.
At the warp gates, the rest of the Shel'na Kryhas, along with a number of Tal'darim who had defected along with Alzadar arrived. The protoss (and fugitives), zerg and Dominion forces weren't able to come to grips with one another, due to the arrival of Ulrezaj himself, who wished to capture Zamara and punish his former followers.
Ramsey convinced the protoss to use a dangerous technique, stopping Ulrezaj long enough to escape through the gate. Some of the renegade Tal'darim entered the warp gate with the two terrans, but none of the Shel'na Kryhas made it through. Stewart's zerg pursued Ulrezaj into the caverns, killing his guardians and forcing him to flee in a xel'naga vessel to the moon of Ehlna. The zerg were, in turn, secretly followed by Dominion forces.