The Protoss Dark Prelate Zeratul continued his investigation regarding a creature called Samir Duran who was also known as Emil Narud to humans. He was contacted by Praetor Talis and led a handful of troops to liberate captive Templars held by Moebius Corps that was human organization serving the Dark God, Amon, also known as the Fallen Xel'Naga. After Zeratul did so, he traveled to the Temple of Erris in Atrias that was guarded by the Tal'darim, a group of Protoss that worshiped Amon led by Highlord Ma'lash. The Dark Prelate discovered the Highlord was communicating with his master via Void catalyst that he destroyed afterwards. Talis and her troops sacrificed themselves allowing Zeratul to escape to warn Hierarch Artanis.
Though Zeratul got the warning to Artanis, the hierarch commenced the invasion to retake the Protoss home world of Aiur. During the invasion, there were hybrids fighting alongside the Zerg that were occupying Aiur. After the Protoss ground forces freed the warp conduits of infestation, Artanis sent the Dark Prelate to retrieve the Keystone also known as the Xel'Naga artifact from their old friend, Jim Raynor. The Dark Prelate found that his Void Seeker was destroyed and a number of Protoss become corrupted. Amon possessed Artanis and was responsible for the corruption of the Khala that was supposed to unify the Protoss. Zeratul succeeded freeing Artanis from Amon's influence by severing his nerve cords but it costed his life. After the hierarch rescued a Phasesmith Karax whose nerve cords were already severed, Artanis and the uncorrupted Protoss activated five power cells so that they could escape the planet via a ship, Spear of Adun. Rohana, a Protoss preserver, had woken from stasis and aided Artanis onwards.
First, Artanis traveled to Shakuras and was contacted by Vorazun, daughter of Raszagal and current matriarch of the Dark Templar also known as the Nerazim. According to her, Amon's Zerg had arrived to the planet through the warp gate on Aiur. Artanis' forces and the Dark Templar cleared the launch bays for her people to evacuate. They also defended the Xel'Naga temple while letting more of Amon's forces to come in billions. Artanis personally overloaded the Xel'Naga temple destroying the planet killing billions of Zerg and hybrids. Vorazun pledged herself and her people to Artanis' cause.
Artanis and his Protoss troops traveled to Glacius where the Tal'darim led by First Ascendant Alarak attacked the research facility in orbit. Artanis' forces managed to recover the technology vault that had data on the Purifier program and there was a prototype warrior inside. Karax discovered that the prototype Purifier had encoded memories of Fenix who remembered being ordered to go to Glacius and to be put on stasis.
Artanis' army traveled to Korhal in order to get the Keystone from Raynor, however Moebius Corps attacked the Sky Shield platform. First, the Protoss cleared enemy troops in the platform so that Raynor's men could repair the stabilizers before it could crash into Augustgrad. After the platform was stabilized, the Moebius Corps seized the Keystone and had hybrids using it to disrupt humans in the battle on Augustgrad. Raynor's men and the Terran Dominion were not the only humans being disrupted by the artifact; it also affected the Moebius Corps as well. Artanis' forces had to hold off the hybrids and helped gaining ground for his human allies. Despite the combined forces drove the Moebius Corps and the hybrid out of the planet so that Artanis could retrieve the Keystone, Augustgrad was in ruins with many dead men. After Artanis and Raynor having a moment, the hierarch was warped into the Spear of Adun while the Dominion were recovering from the havoc. Raynor's chief engineer Rory Swann sent Artanis the data on Narud and the Keystone.
Artanis and his army traveled to Ulnar to find the Xel'Naga. They activated five celestial locks to gain entry into the temple while holding off both the Tal'darim and Moebius Corps. Artanis decided to enter alone and Sarah Kerrigan known as the Queen of Blades was attacked by a hybrid. After the two slew the monster, they explored the temple together. While fighting the Tal'darim, Moebius Corps, hybrids, and the temple sentinels; Artanis and Kerrigan learned more about the Xel'Naga. When they reached the chamber, they were shocked to find all of the Xel'Naga were slain by Amon who was creating a host body on Aiur using both Protoss' flesh and Zerg's essence. Alarak boarded the Spear of Adun and had a brief fight with Vorazun. The First Ascendant stated Amon had betrayed his people and he wanted retribution. After rescuing Artanis and Kerrigan, the combined forces battled their way through the other Tal'darim and Moebius corps to destroy four Void Crystals. Kerrigan decided to rebuild her Swarm leaving Artanis to gather allies and he had uneasy dealings with Alarak.
Artanis and his army traveled to Slayn because Alarak promised to remove the Tal'darim from the conflict. First, Artanis' forces had to fight through a Terrazine fog to destroy three guardians of Ma'lash before Alarak could challenge Ma'lash in the ritual of Rak'Shir. During the ritual, both Alarak and Ma'lash would not be damaged by the other Protoss. Nevertheless, Artanis' army and the army of Ma'lash including hybrids provided psionic support. Artanis' forces defeated the forces of Ma'lash so that Alarak could win by pushing Ma'lash into a death pit. After Alarak became a new leader of the Tal'darim, he rallied the remaining Tal'darim to Artanis' cause and to destroy Amon for the betrayal.
Artanis and his army traveled to Endion that was occupied by Amon's Zerg to activate Cybros. First, they used a device Megalith to work its way in five stasis locks to deactivate Cybros' shields. Artanis' forces had to battle the Zerg in Cybros station to activate the Purifiers that purged the Zerg of Endion and the Purifiers agreed to join Artanis after he promised that they would be treated as equals.
Artanis and his army tracked the Moebius Corps to their base in the asteroid field of Revanscar. The Spear of Adun was attacked by Moebius' fleet and Karax had to command his fleet of Carriers to destroy three power generators. Karax succeeded destroying the Moebius' facility along with its hybrid program and was promoted to Templar.
Artanis and his army returned to Aiur. First, two Khaydarin Crystals powering the Psionic Matrix are to be destroyed in order to delay the corrupted Golden Armada. Alarak and Vorazun destroyed the first in Antioch; Karax and Fenix who later named Talandar took out the second in the ancient temple grounds; Artanis destroyed the last the Xel'Naga caverns. After Artanis' army destroyed the Void Shards to destroy Amon's host body, they defended the Keystone from the combined corrupted Golden Armada and Amon's Zerg long enough for it to gather sufficient energy to force Amon out of the Khala. Artanis' forces succeeded and freed the other Protoss from corruption by causing Selendis' and her troops to sever their nerve cords. After they did so, Amon had retreated to a secret planet in the edge of the Korprulu Sector.
Raynor realized something was glowing and it turned out to be a stone that was given to him by his wizard friend, Gandalf the Grey. The Free Peoples called for aid, he thought. He also received a transmission from Kerrigan who tracked Amon to the planet. Raynor and Matt Horner took a handful of men to Middle-Earth. On orbit above Middle-Earth, the Swarm had arrived along with the Protoss as Artanis had received a similar transmission. The leaders: Raynor, Kerrigan, and Artanis had a meeting on orbit. "So, this is the planet that Amon went to which is the one we haven't been to," said Artanis.
"This planet is called Middle-Earth. I have been to that planet long before the first time we met," said Raynor.
"What value does Amon hold there?" Kerrigan asked.
"He's helping the dark forces in Middle-Earth. Zeratul told me that Amon and the Dark Lord Sauron are in league," Raynor stated the fact remembering what the Dark Prelate told him.
"How come?" Artanis asked.
"Amon first had to wipe us out before helping Sauron to achieve domination of that planet. The Dark Lord of that planet see us as threats to his conquest," Raynor guessed the Dark God's plan.
"Who is that Sauron guy? I heard that name before," Kerrigan asked.
"He was the one who started the war on that planet years ago. It began with forging of the great rings of power. Nine were given to us humans, three to the elves…" Raynor began explaining recalling what Elrond and Galadriel told him about the history.
"Elves? This is starting to become a fantasy here," Kerrigan interrupted.
"What are elves?" Artanis asked.
"Humans with pointy ears," Kerrigan replied.
"The elves are the fairest and immortal of all beings. Seven to the dwarf lords …" Raynor continued.
"Dwarves?" Artanis spoke in disbelief.
"Short humans like Rory Swann for example. The Dark Lord Sauron had forged in secret a master ring from the fires of Mount Doom to control all others. From this ring, he committed numerous atrocities to dominate all life. An alliance of humans and elves marched against the armies of Mordor on the slopes of Mount Doom; they fought for the freedom of Middle-Earth. From what I heard, Sauron was the most deadly adversary in Middle-Earth. He could kill multiple foes within a single swing from his mace and one of the victims was the human king Elendil. Though the Dark Lord shattered the king's sword and was about to finish the king's son Isildur, his fingers were sliced off disconnecting the ring from him by Isildur using the broken sword. Sauron appeared to be vanquished but his spirit endured and he's still alive," Raynor finished recalling the history.
"How can this possible?" Artanis could not believe it.
"What happened to Isildur?" Kerrigan asked.
"The ring betrayed him to his death and was lost in depths of the Anduin River," Raynor replied.
"That's a lot to take," Artanis commented.
"I'm going to Bag End," Raynor made his decision.
"Let me come with you," said Kerrigan.
"Perhaps we can explore the place," said the Protoss hierarch.