End War

A war against Amon was waged by the Protoss Protectorate in response to the threat the fallen xel'naga posed to the Milky Way. For clarity's sake, it is kept separate from the conflict that was waged by Amon in the vision glimpsed at through the Overmind and through it, Zeratul and Tassadar,

Background
The Second Great War paved the way for Amon's return. The use of a xel'naga device on Char de-infested the Queen of Blades, returning her to terran form. It was speculated by Alexei Stukov that it was this act that had allowed Amon to return to life, that hybrids had been present to collect the energy. That Amon was indeed revived was confirmed by Emil Narud, and after the war's conclusion, with the death of Arcturus Mengsk, Kerrigan (again the Queen of Blades, albeit in primal form, led the Zerg Swarm to find and confront the fallen xel'naga. That Kerrigan was alive at all was potentially a divergence from the future glimpsed at through the Overmind's vision, in which case her death had led to the protoss's final defeat.

Largely removed from the conflict between the zerg and Terran Dominion however, was the Protoss Protectorate, which was dealing with internal issues. The Khalai and Nerazim which made up the Daelaam were sliding into tribalism, prompting Hierarch Artanis to launch an effort to reclaim Aiur. The rationale was that reclaiming the planet from the zerg was the only shared interest possessed by both branches of the protoss, and through doing so, a new civilization could be built from the rubble of the old. The Golden Armada, the largest fleet of protoss warships ever constructed, was created with the explicit purpose of reclaiming the lost protoss homeworld. In 2505, not long after the conclusion of the Second Great War, the fleet was launched.

The Reclamation of Aiur
"Today we will reclaim our homeworld!"

- Hierarch Artanis

The Golden Armada arrived at Aiur. However, the invasion went awry as Amon revealed his presence to the protoss, corrupting the Khala. Artanis and his followers were forced to sever their nerve appendages and flee in the Spear of Adun.

In the aftermath of the Battle of Aiur, Amon unleashed legions of hybrids in a galactic assault.

The Battle of Korhal
The Shadow Corps attacked Korhal's space forces and also sabotaged the Sky Shield space platform, sending it hurtling down towards Augustgrad. Artanis arrived at the planet at the behest of Zeratul, where on the Sky Shield he provided support to Dominion forces under the command of Jim Raynor. Augustgrad itself also came under attack, suffering heavy damage.

The Battle of Shakuras
Matriarch Vorazun contacted Artanis, informing him that Shakuras had come under assault by zerg that were under Amon's control. Artanis's forces cleared launch bays so that Vorazun's ships could escape. The battle escalated as a void thrasher was unleashed against the protoss.