The End War, also called the Final War, was a term used by Zeratul to describe the crusade waged by Amon against the Daelaam, and galaxy as a whole. 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.
The Second Great War
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. Amon's resurrection 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 her death had led to the protoss's final defeat.
Largely removed from the conflict between the zerg and Terran Dominion however, was the Daelaam, which was dealing with internal issues. The Khalai and Nerazim 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. As Kerrigan took the Swarm away from the Koprulu sector, the fleet was presented with an opportunity to retake Aiur. Thus, not long after the conclusion of the Second Great War, the fleet was launched.
Prelude to the End War
- Dark Prelate Zeratul(src)
Seeking the last part of the Ulaan Prophecy and the role that protoss civilization had to play in the coming return of Amon, Dark Prelate Zeratul sought out the location where Amon had been revived. However, the last being who knew of its location, Samir Duran, had been slain by Sarah Kerrigan. Zeratul sought to find what information he had one of his Moebius Foundation bases. When he arrived, he found Praetor Talis and her forces besieging the base in order to rescue the templar warriors trapped within. Zeratul agreed to help, but found Kerrigan and her Zerg Swarm attempting to destroy the base. Zeratul raced against Kerrigan's forces, and fought through Moebius Corps and hybrid forces to rescue the trapped templar. Upon freeing the last group, they revealed they had been captured by the Tal'darim, and the Moebius databanks revealed that they had been taken to Atrias in the Sigma Quadrant.
Talis agreed to aid Zeratul in finding the final piece of the prophecy. They landed on Atrias and fought through Tal'darim warriors to reach the Temple of Erris, the main Tal'darim stronghold on the planet. Talis held the enterance to the temple while Zeratul and a small force slipped in. Zeratul moved through the temple, fighting through Tal'darim and hybrid, until he discovered Highlord Ma'lash communing with Amon. Amon ordered him to war, and Zeratul realized it was too late, but that he could delay the Tal'darim if he destroyed the void catalyst they used to commune with him. Zeratul destroyed the catalyst, and through the Void Zeratul heard a voice much like Tassadar telling him the Keystone would usher him unto hope. Amon then attempted to collapse the temple, but Zeratul escaped in the Void Seeker. Talis and her forces sacrificed themselves to buy Zeratul time to escape. Zeratul fled the planet, and sought to contact Artanis to warn him about the coming war.
Course of the War
Reclamation of Aiur
The Golden Armada arrived at Aiur. However, the invasion went awry as Amon revealed his presence to the protoss, corrupting the Khala and turning many of protoss into his servants. Dark Prelate Zeratul of the Nerazim fell to Amon, although he managed to remove Artanis's nerve cords so he could lead the Protoss again. Artanis and his followers severed their nerve appendages and Nerazim were forced to reactivate an ancient protoss arkship, the Spear of Adun, to escape Aiur. The remnants of the invasion force and the fleet not under the influence of Amon escaped aboard the arkship.
In the aftermath of Aiur, Amon unleashed legions of hybrids in a galactic assault. He divided his forces into separate groups as part of his overall strategy to conquer the entire sector all at once. By the opening stages of the war, Korhal, Shakuras, and Glacius had come under attack. Artanis mobilized his forces aboard the Spear of Adun in order to stem Amon's tide, and attempted to find an edge to use against Amon's armies.
The following section contains timeline information which isn't necessarily in chronological order.
The Battle of Korhal
"Call themselves Moebius Corps, an elite guard that used to work for Dr. Narud. They've been striking worlds throughout the sector, leaving few survivors. Each world attacked reported hybrid leading them."
The Moebius Corps, with hybrid leading the way, rampaged across Dominion space before arriving to Korhal in a surprise attack. They managed to seize control of and then sabotaged the Sky Shield space platform, sending it hurtling down towards Augustgrad. Emperor Valerian Mengsk took command of Dominion forces on the ground with a part of the Dominion Fleet in lower atmosphere, while Admiral Matt Horner and Commander Jim Raynor commanded what was left of the defense force in Sky Shield and the Dominion Fleet in orbit with Raynor's Raiders in tow. 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 with fire support from the Spear of Adun. Augustgrad itself also came under attack, suffering heavy damage. In the midst of the battle, the Keystone was stolen by the Moebius Corps after a raid on the Korhal Palace, where it was taken to Bennet Port for extraction. Dominion and Daelaam forces managed to overcome the Moebius and hybrid forces, though the battle left Augustgrad in ruins. The artifact was handed over to the protoss.
The Fall of Shakuras
"Matriarch Vorazun, what has happened here?"
"Shakuras has fallen! The warp gate linking this world to Aiur has been reopened. Countless hybrid and zerg pour from the other side! They've obliterated our cities. Decimated our Shadow Guard. We're trying to evacuate the remaining population, but I am uncertain whether we can hold long enough to get them safely away."
Matriarch Vorazun contacted Artanis, informing him that Shakuras had come under assault from millions of Amon's zerg pouring through the warp gate to Aiur. The Nerazim were pushed back with heavy casualties, and most of Talematros was overrun. Artanis's forces cleared launch bays so that Vorazun's ships could escape. The battle escalated as Void thrashers were unleashed against the protoss. Launch bays were later cleared and the survivors managed to escape Shakuras and rejoined the Spear of Adun. Matriarch Vorazun, however, did not want Shakuras to become a staging ground for Amon's armies, and persuaded Artanis to destroy Shakuras using the planet's xel'naga temple. Artanis agreed and also planned to wound Amon's forces by luring in as much of Amon's zerg brood to Shakuras as possible. Daelaam defenders held the line as the temple's phase prism was set to overload before entering the planet's core. The line was held successfully, and the core was dropped, destroying Shakuras, and over 1 billion of Amon's zerg.
The Battle of Glacius
In order to help gain an edge against Amon, Artanis took the Spear of Adun to the Khalai Caste research base on Glacius, where scientists were developing a new Purifier program. However, as the Daelaam arrived they found the Tal'darim under First Ascendant Alarak assaulting the facility. The Tal'darim fired on the facility using their mothership's displacement beams, intending to destroy the facility's technology vault.
Artanis mobilized his forces the surface, racing the displacement beam to the vault while Tal'darim defenders turned the facility's defenses against the Daelaam. The Daelaam were successful in reaching the vault before it was destroyed, taking the container containing data on the new Purifiers aboard their arkship. This act impressed Alarak, who stated they would meet again. Aboard the Spear of Adun, Karax found a complete prototype Purifier program within the sphere modeled off of the memories of Praetor Fenix, who only had memories up until Fenix's revival as a dragoon. Artanis was happy to see his old friend, but melancholy as he pondered whether the construct was truly the Fenix he knew.
Revelations at Ulnar
"Zeratul was right... It is Ulnar. Think of it, Matriarch, the cradle of all life hidden all these years."
"Yes... But why?"
- Artanis and Vorazun(src)
Karax's studies of the Keystone identified its point of origin in the Altarian Rift, where it was believed the xel'naga resided at Ulnar. Arriving at the structure, the Daelaam defeated the Tal'darim and Moebius Corps forces present to unlock the temple's inner vaults. Artanis went there alone, and encountered Kerrigan in the temple; Kerrigan faced against many hybrids in the vault, and was incapacitated when one appeared. However, Artanis distracted the hybrid long enough for Kerrigan to kill the hybrid, and they were forced to create an uneasy alliance. Reaching the center of the vaults, Artanis was shocked to learn that most of the xel'naga had been killed, and Amon had opened a door to the Void. On the Spear of Adun, First Ascendant Alarak appeared there, and forced Matriarch Vorazun to an uneasy alliance to help Artanis, as Alarak felt that the Tal'darim were betrayed by Amon. Reaching Artanis, the Daelaam and the Swarm closed the door to the Void and were forced to retreat. Kerrigan suggested to Artanis to subjugate enemies and gather allies in order to defeat Amon.
The Tide Turns
After Ulnar, the leaders of the Daelaam met to discuss their options. Alarak pressed the issue of the Tal'darim Death Fleet, and how he could bring his people into the fold if the Daelaam helped him in becoming Highlord. Fenix brought up the purifiers of Cybros, how they could be useful allies in the looming battle. There was still the issue of Moebius Corps, who were operating from a hidden base. However, it had to be found first, and Vorazun dispatched scouts to find its location. Artanis was thus presented with the immediate choice of heading to Cybros or Slayn. In the meantime, Amon took the Golden Armada under his control and let it loose against the Dominion, while sending his zerg against Daelaam colony worlds and dividing his forces to conquer separate parts of the sector. 
The following section contains timeline information which isn't necessarily in chronological order.
Alliance with the Tal'darim
"Behold, the death fleet under Amon's command, poised on laying waste to all life in this sector."
"Then we had best act swiftly."
- Artanis and Alarak(src)
The Spear of Adun arrived at Slayn. Alarak intended to depose Highlord Ma'lash through Rak'Shir, thus bringing the Tal'darim under his thrall. Templar forces were deceived by Alarak into eliminating Ma'lash's guardians, as Alarak knew they would have sided with the highlord in the duel. Artanis seethed at the deception, but nonetheless let events unfold. With the aid of the Daelaam, Alarak defeated Ma'lash through Rak'Shir, and become highlord of the Tal'darim. The two agreed to continue their alliance.
Ending Moebius Corps
Artanis quickly moved to destroy the last hybrid production facility in the Revanscar asteroid system, hoping to destroy Amon's hybrids. As the Spear of Adun was too big to enter the asteroid field without damage, Karax put forward that protoss carriers can get close enough to destroy the power relays to the facility and thus the facility itself. As they arrive to Revanscar, however, Moebius Corps attacked the Spear of Adun, sending hybrids and cloaked spectres into the ship, and sending multiple battlecruisers in a surprise attack. Artanis, Vorazun and Alarak leads the defense forces of the Spear of Adun, so Karax was sent to lead the carriers to attack the station. At first, Karax was unsure of Artanis's command, as he was a Khalai Caste phase-smith, but Artanis believed that Karax's knowledge of the station's defense will be of more use. Karax successfully destroyed the station, stopping the hybrid productions and reported back to the Spear of Adun, while Artanis managed to repel the Moebius attacks.
After the victory at Revanscar, Karax was summoned before the council in the Spear of Adun, with Artanis proclaiming that the age of the Khalai Caste system is at an end, that anyone can be a Templar through their actions, not just by birth. With this, Karax became a Templar, and the Caste system ended.
Reactivating the Past
Artanis knew that Khalai scientists were researching new technology for the Daelaam, one of which was the reactivation of the Purifier weapons program. While Grand Preserver Rohana considers this heresy, as the Purifiers betrayed the Conclave ages ago, Phase-smith Karax convinced Artanis that if the Purifiers were treated as equals, they would help the Daelaam. On Glacius, they managed to gain the facility's research and an experimental prototype; the prototype was revealed to be based on Artanis's old friend Fenix, who was killed by the Queen of Blades. After the battle in Ulnar, Artanis set out to the forest moon of Endion, where the Cybros space platform, home of the Purifiers, is located. After disabling the moon's defense grids for Cybros, the Daelaam reactivated Cybros and awaken the Purifiers in the facility. Cleaning the facility of zerg, the Purifiers then "purified" Endion due to high zerg infestation. Artanis then promised that the Purifiers would be treated as equals among the Templar, and the Purifiers agreed to help the Daelaam, as long as Fenix became their representative on the Spear of Adun.
Return to Aiur
- Hierarch Artanis(src)
With the Purifiers in tow, the Tal'Darim allied to them and the hybrid facilities destroyed, the Daelaam prepared for the second reclamation of Aiur. There are problems however: they would need to destroy Amon's physical body, and destroy the psi-matrix around Aiur to halt the Golden Armada to help Amon. Artanis decided to divide his forces: Alarak and Vorazun destroyed one in the Citadel of the Executor, Fenix and Karax destroyed another in the Ancient Temple Grounds, while Artanis himself leads a team of zealots to destroy the last one in the Xel'naga Caverns. They all succeeded, and then mounted an attack to destroy the Void structures feeding energy to Amon's body. With the body not feeding on Void energy, the body was forced to be released early. Artanis then ordered the Tal'Darim death fleet, Cybros and the Spear of Adun to unleashed their entire firepower to destroy the body, and they succeeded.
Setting the xel'naga keystone on the temple grounds, the Nerazim, Purifiers, Tal'darim and Khalai held the zerg and the influenced protoss back. As they held back since the keystone was ready, Executor Selendis and the protoss were freed for a while against Amon, and Artanis managed to convinced the Templar to free themselves.
With this victory, the Daelaam became united, and set to rebuild Aiur as a unified protoss, and set to reclaim their destiny among the stars. Artanis then created a grave for Zeratul and set his psi-blade down and promised a unified protoss.
In 2508, during the celebration of the reclamation, Kerrigan sent a transmission to the Spear of Adun and the Hyperion: to both Artanis and Jim Raynor, requesting help to destroy Amon. Artanis set out with Selendis on the Spear of Adun and parts of the Great Fleet; Jim Raynor set out with Matt Horner on the Hyperion, but Valerian Mengsk was needed on Korhal, so he sent a squadron of Dominion battlecruisers to assist Raynor; while Kerrigan recalled her broodmothers from the Swarm back to Ulnar. Meeting on the Spear of Adun's War Council, Artanis and Raynor agreed with Kerrigan to destroy Amon once and for all; and with this declaration, the alliance of terrans, zerg, and protoss entered the Void.
On entering, protoss forces destroyed a Void tower that was halting the terran advance, and with it, terran and zerg bases were set up. Greeting them on the entrance of the gateway was Emil Narud, now revealed as xel'naga. Kerrigan then sent for Alexei Stukov, who has a grudge against Narud when he was killed by Narud as Samir Duran. The allied forces then advanced on the temple grounds, securing advanced positions to muster their forces. As the Void forces cleared, Stukov stand before Narud, and took his revenge by killing Narud. Narud's death freed the last xel'naga to oppose Amon, Ouros; he was disguised as Tassadar's ghost, surprising Artanis. Ouros then revealed that only Kerrigan can defeat Amon, since she's the only one that can handle the transformation to a xel'naga. As the alliance held back Void forces, Kerrigan gained the essence of a xel'naga and became one herself. With this power, she went to face Amon, backed by the entire alliance.
The alliance facing Amon helped Kerrigan destroy seven Void crystals shielding Amon, and she then confronted him herself. Declaring the universe free from his threat, Kerrigan destroyed Amon with a powerful beam of energy. As Amon exploded in a blinding flash of light, Kerrigan ordered Raynor and the others to flee.
The following section contains timeline information which isn't necessarily in chronological order.
The following battles are known to have occurred during the conflict, but their timing in relation to the above events (and each other) is unclear.
- Dominion worlds were attacked by Moebius Corps, led by the hybrid, laying waste to many planets and outposts while leaving a horrific toll of casualties in their wake. After the defense of Korhal however, Dominion forces eventually managed to repel Moebius.
- Nerazim troops scouted the worlds around Aiur, helping those who escaped the carnage of Amon's forces.
- At least one Daelaam colony world managed to escape in time from the onslaught of Amon's forces, though not before bearing witness to the fall of other neighboring systems.
- In the aftermath of the events on Ulnar The Golden Armada, under Amon's influence, began attacking Dominion worlds after Moebius had been repelled. Even though Dominion defenses were now more solidified, they were stretched far across the Dominion, and many worlds fell to the Armada. As the war continued however, the Dominion managed to reclaim these worlds due to the Armada being recalled back to Aiur.
- On Char, Amon's forces engaged terran forces under the command of Sergeant Bama Kowalski, utilizing void thrashers. Allied forces were dispatched to liberate her base and take out the creatures.
- A battle was fought on Kaldir, where Amon's forces attempted to escape through warp conduits, but were intercepted.
- Korhal Palace was besieged by Amon's forces, who attempted to use void shards to devastate Augustgrad. Allied forces destroyed these shards.
- Moebius Corps attempted to use the railway on Tarsonis to ferry cargo, but this was intercepted by allied forces.
- After Alarak's ascension to Highlord, First Ascendant Ji'nara was challenged to Rak'Shir by a splinter faction of Tal'darim still loyal to Amon. With the help of allied commanders, Ji'nara was able to defend her rank on the Chain of Ascension.
- Egon Stetmann, abandoned on Bel'Shir after the fall of Arcturus Mengsk, and his terrazine research operation came under attack by Amon's forces. He called on two allied commanders to defend his harvesting operation. The commanders were successful at defending his harvesting bots, allowing him to get the terrazine he needed to leave the planet.
- Amon's forces assaulted the planet of Veridia Prime, using a device to cause the planet to meltdown. Emperor Valerian Mengsk tasked allied commanders with retrieving twenty xenon crystals and using them to activate the planet's environmental stabilizer before Veridia Prime was destroyed. Donny Vermillion of Universal News Network reported on the conflict as it developed. Amon's forces were defeated, the stabilizer was reactivated, and the planet was saved.
- On a fringe Kel-Morian Combine colony, Amon unleashed a powerful infestation on the colonists. Guildmaster Debra Greene called upon allied commanders to aid in the colony's evacuation. The colonist's shuttles were defended from the infested, allowing them to escape the planet.
- At the colony of Chazington, a powerful outbreak of zerg infestation hit, supported by Amon's forces. Lieutenant Rosa Morales arrived to stem the infestation, but found it would be too late to evacuate the colony. She called on two allied commanders to stem the infestation. The commanders fought through waves of infested and purged the colony.
- Amon moved forces onto a populated protoss world, and took hold of the planet's xel'naga temple. He summoned void slivers in an attempt to channel Void energy into the temple to summon a voidshade hybrid. A Nerazim scout named Lyrak discovered the operation, and brought in allied commanders to destroy it. The commanders were successful in destroying the slivers, then bombarding the temple and destroying any chance of summoning the hybrid.
- General Carolina Davis personally commanded an archangel into a Moebius Corps base where they were breeding powerful Moebius hybrid, and called on the aid of two allied commanders. Together, they were able to exterminate the hybrid.
- As the Purifiers began to activate, one facility began to become corrupted as a Tal'darim personality was let loose in the facility. One of the facility's personalities named Aurana called on allied commanders to help her purge the facility of the AI. Aurana was successful in eradicating the AI from the facility.
- Ghost agent Stone was dispatched by the Dominion to investigate a Moebius Corps battle station augmented by xel'naga technology located near several colony worlds. Allied forces were called in to use xel'naga artifacts to destroy the station before it opened fire on the colonies.
- Some years after the first battle on Bel'Shir Stetmann returned to the planet with Gary, and fought Amon's forces alongside an allied commander to gather terrazine from the planet.
- In 2508, Amon sent forces to destroy Ulnar to prevent the Korpulu factions from entering the Void. Under the guidance of Grand Preserver Rohana, Ulnar's locks were secured before they could be overloaded.
Two years after the battle on Aiur, Emperor Valerian Mengsk and Admiral Matt Horner led the Dominion to a new age of peace and prosperity, with support from the Dominion's military. Jim Raynor disappeared mysteriously, with only his badge found at Joeyray's Bar on Mar Sara. The protoss, now unified under the Daelaam, continued to rebuild Aiur and held peaceful relations with the Terran Dominion. The Tal'darim declined an alliance with the Daelaam and departed to find a new world, with Alarak giving one chance for any of his Tal'darim to remain on Aiur. The zerg, now led by Zagara, reclaimed Char and the surrounding worlds. Meanwhile, life began to bloom on previously barren worlds, baffling Dominion scientists.
By 2511, both the Dominion and Daelaam were struggling to rebuild from the conflict. The Dominion had to deal with a food shortage, as much of its croplands had been destroyed in the war, as well as a plethora of veterans suffering from psychological trauma. The Daelaam also experienced a cultural shift as a movement harkening back to the Golden Age of the protoss was sparked by the Shelak Tribe; by embracing their glorious past, they hoped to quieten their fears about an uncertain future. The movement was embraced by many Templar, but it provoked tensions with the Nerazim, as the Templar appropriated some of their own technology, redesigning it to invoke the Golden Age. Vorazun refused to comment on the issue, and the movement received no official acknowledgement by the leadership of the Daelaam.