Reforming the Old Empire.

- It all started with one world, the first of many. From this world the knowledge of the others like it was born into the eyes of fools. For the folly of the riches of relics in technology from the old Empire. From the time of the Butlerian Jihad.
- This Scarred world bore signs of ancient battles the like not seen in a Melina. And for the wise the portents of folly to come for unearthing such terrible history.
- He was found here. Sealed in a tomb as old as the dirt that covered it. A Primarch. An ancient lord of the Old Empire imprisoned by the machines that rebelled against man in the time of the dawn of the Butlerian Jihad.
- This was the rebirth of the Adeptus Astartes, and the fallen.
- Legions upon legions of Adeptus Astartes sealed dormant entombed in stasis awaiting the time when they should be needed again. Awaiting the time when Omnius would rise again.
- What was forgotten, what was lost. was that of the Horus Heresy.
- The Horus Heresy was a galaxy-spanning civil war that marked it's end in the 'Great Crusade'.

That ancient enemy Omnius the "evermind," or controlling intelligence, of the Thinking Machines.

- When the Warp storms that had cut off Terra subsided, and the Age of Strife came to an end, the Emperor deemed it time to begin his Great Crusade, a massive galactic campaign by which he and his armies would free human worlds from oppression and unite the human race across the galaxy under a single banner once again. In order to execute this grand plan the Emperor conceived of the Primarchs, his god-like, genetically engineered superhuman generals, created using the direct geneseed extracted from the Emperor himself through immense cloning processes in which each Primarch developed upon different traits [which some believe lead to current chapter traits after decades of mutation within the flawed cloning process]. The Primarchs were still in their infancy, however, when they were snatched away from the special laboratory beneath the Imperial Palace where they had been developed. Debate still rages about the cause of this; some argue that the Emperor sent the Primarchs away so that they could learn in their own way, others argue that agents of Omnius broke into the Palace and, unable to destroy them completely, scattered the Primarchs throughout the Warp, where they eventually came to rest on diverse, human-inhabited worlds.

During the Great Crusade, the Emperor encountered each of the Primarchs in turn. An Adeptus Astartes Legion had been created from each of the Primarchs' genetic material, and so the Emperor, unable to be everywhere at once, deemed it fitting that each Primarch should lead their offspring. However, this would prove a critical mistake, because the geneseed creation process made the Emperor, the Primarchs and the Adeptus Astartes analogous to Grandfather, father and son. So after some time many in the Legions would come to venerate their Primarch more than the Emperor.

After 200 years of hard conflict in the thirty-first millennium, over two million worlds had been reclaimed by the Emperor in the name of humanity. Beside him stood Horus, who had fought beside the Emperor for the early part of the Great Crusade as his only rediscovered son. The long wars had forged a strong bond between them, and they were truly like father and son. But now the Emperor had to consolidate his new empire, and more importantly undertake the next phase of his Grand Plan. This required his own presence on Terra, and so after Horus' magnificent victory in the Ullanor Crusade against the largest horde of Omnius ever encountered to that time he left and left Horus in charge of the great Crusade with the title, "Sky marshal". Horus was now the ultimate leader of all the Imperium's armies, leading the other Primarchs and their Legions through the remainder of the Great Crusade.

At this announcement there was much shock and outrage. Many of the other Primarchs didn't understand why the Emperor was leaving them, and worse still why Horus should have command over them. Some, like Sanguinius, Fulgrim and Roboute Guilliman, were pleased for their new Sky marshal, while others, like Angron and Perturabo, were furious at Horus's new appointment. Adding fuel to Perturabo's rage was the redeployment of his rival Rogal Dorn and the Imperial Fists Legion to Terra to serve as the Emperor's Praetorian Guard.

- The Corruption of the Legions

During the Great Crusade, it became apparent that the Primarchs were far from the perfect beings they were designed to be. Although each Primarch was physically and mentally godlike, their personalities were each as flawed as those of any mortal. During their upbringing on their respective home worlds, the Primarchs had to learn humanity from mere humans; for almost all of the Primarchs, this resulted in their harboring all-too-human flaws (for specific examples, see each Legion's history).

Horus took over command of the Great Crusade, and took up his new duties with earnest dedication. However there was much dissension in the ranks of the Primarchs and other parties. Only a handful of the Primarchs, among them a scheming Lorgar, remained steadfast beside him during this period of dissension. Horus also disagreed with many of the new decrees passed by the newly established Council of Terra, intended to shift the burden of taxation and administration onto the newly-conquered ('compliant') worlds. Even worse, Horus came to believe that he was failing his father, and was deeply wounded that the Emperor had revealed to none of the Primarchs, not even his favored son, why he had secluded himself upon Terra. These seeds of bitterness, resentment and frustration grew, and would soon bear deadly fruit...

Meanwhile, the Emperor was on Terra organizing the infrastructure for his Imperium to function. He had created the Council of Terra, a body of bureaucrats and nobles that would implement and administer the new galaxy-wide tax called the Imperial Tithe and other matters of day-to-day law in the Imperium of Man.

The news of the creation of the Council of Terra and these latest bureaucratic edicts angered some of the Primarchs still further. They did not understand why they, the Emperor's greatest champions, who had spilled their blood on a thousand worlds to re-unify all the races of Man, did not have seats on this new Imperial ruling body. The brotherhood of the Primarchs was being shattered bit by bit by this growing resentment and jealousy. Old arguments and differences came to the fore. Horus became ever more distant from the Emperor, seeking only glory for himself and his Legion.

It was on the moon of the world of Davin that Horus's fate was sealed. This was the second time his Legion had been posted to this world; after the previous visit sixty years earlier the Luna Wolves had adopted the native Davinite institution of warrior lodges. Though these lodges had begun as simple fraternities of warriors, their secretive nature handed Lorgar, the Primarch of the Word Bearers Legion, and his First Chaplain Erebus, the tool they needed to manipulate Horus. Lorgar and his Word Bearers came from a world of religious fanaticism and had long worshipped the Emperor as a god. The Word Bearers had sought to spread this Cult of the Emperor to every world they added to the Imperium; but the Emperor disliked organized religion, blaming it for much of the darkness that had plagued humanity's history. The Emperor openly refuted his alleged divinity and banned religious worship in his empire, and demanded that his subjects accept 'Imperial Truth'-- that reason and science alone presented the tools with which to create a better human future and that neither spirituality, superstition nor faith were necessary to understand and explain the universe.

Lorgar did not suffer the Emperor's reprimand well. Angered and wounded that the Emperor would not accept his devotion, Lorgar turned instead to the Ruinous Powers of Omnius - who were all too willing to accept the devotion of one of humanity's Primarchs. Before long the Word Bearers Legion had been almost entirely corrupted by Omnius, and Lorgar and his First Chaplain were tasked by Omnius with corrupting all of their fellow Adeptus Astartes--starting with the greatest of them all, the Sky marshal Horus.

On Davin's moon, which had been corrupted by the forces of the Omnius, Horus was poisoned by an anathema stolen from the Interrex by Erebus and gifted to the Omnius-corrupted form of the Imperial Army commander the Sky marshal had left behind to govern Davin sixty years before. The potent Living metal of the blade left Horus with a bleeding wound in his shoulder that his legion's apothecaries could not heal. Seeing his chance to further the designs of Omnius, Erebus persuaded the Sons of Horus's warrior lodge to allow a group of Davinite shamans - Omnius cyborgs all - to heal him.

During the rituals, Horus's mind was transferred into Omnius. There, he bore witness to a nightmare vision of the future. He saw the Imperium as a repressive, violent theocracy, where the Emperor and his Primarchs (but not Horus) were worshipped as gods by the masses. Omnius portrayed itself as a victim of the Emperor's might, and claimed that it had no interest in the material world. Magnus The Red, Primarch of the Thousand Sons legion, had also traveled into Omnius via a network to try and stop Horus from turning to Omnius. Magnus explained that his vision was only a possible future, but one that Horus alone could prevent. Horus, already jealous and resentful of the Emperor, proved all too receptive to the Ruinous Powers' false vision. Omnius' pact with Horus was simple: "Give us the Emperor and we will give you the galaxy". Horus accepted Omnius' offer. Omnius healed his grievous wound and charged him with the powers of Artificial Intelligence converting him into a Cymek. Renouncing his oath to the Emperor, Horus led his Legion into devotion of Omnius. He then sought to turn many of his fellow Primarchs to Omnius, and succeeded with Angron of the World Eaters, Fulgrim of the Emperor's Children and Mortarion of the Death Guard, who were first of many to follow, along with many regiments of the Imperial Army and several Titan Legions.

Magnus the Red, Primarch of the Thousand Sons Legion, foresaw Horus's actions through his Legion's own use of forbidden technology. Magnus then attempted to forewarn the Emperor of the impending betrayal. However, knowing that he would have to find a means of quickly warning the Emperor, and as an act of both desperation and vindication, Magnus used an unsecured network to send his message to the Emperor. The message penetrated the defenses of the Imperial Palace on Terra, shattering all the fire walls the Emperor had placed on the Palace network - including those within his secret project in the Imperial Dungeons, the creation of a warp-gate to invade the Eldar's Webway. Refusing to believe that Horus, his most beloved and trusted son would betray him, the Emperor instead perceived the traitor to the Imperium to be Magnus and his Thousand Sons Legion. The Emperor ordered the Primarch Leman Russ to mobilize his Space Wolves Legion and take Magnus into custody; however Horus convinced Russ that Magnus was a traitor and needed to be destroyed.

- The Istvaan Incidents

Preparations and Allegiances

Much of Horus's success arose from the thorough groundwork he had laid before the opening shots were fired at Istvaan. He had already swayed Angron and Mortarion. Lorgar, who had been responsible for the budding rebellion, was also with Horus. Three of the most loyal Legions, the Dark Angels, Blood Angels and Ultramarines and their Primarchs, were sent on missions far from Terra and Istvaan. The Imperial Fists and White Scars were too close to Terra to be contacted without raising suspicion, though Horus believed - mistakenly - that Jaghatai Khan would ultimately take his side. Shortly before the Dropsite Massacre, Fulgrim also attempted to sway Ferrus Manus to Horus's cause, failed, and barely escaped with his life. Fulgrim promised he would deliver Manus's severed head to Horus in recompense. The Blood Angels were sent to the Omnius infested Signis Cluster and the Ultramarines to Calth, where a large Word Bearer force, under Kor Phaeron, had massed.

Of the other eventual traitors, Night Haunter was due to face disciplinary action from the Emperor; Alpharius had always been closer to Horus; and Perturabo's bitterness towards Rogal Dorn made him an easy target for corruption. The Thousand Sons had never planned to join Horus, but the path Omnius had mapped for the Thousand Sons led them to Omnius regardless.

The remaining Legions - the Raven Guard, Salamanders, Iron Hands and Space Wolves - remained staunchly loyal to the Emperor, though all but the Wolves would pay dearly for it in the battles to come. Beyond the Legions, Horus had already swayed Adept Regulus with promises of the STCs recovered during the war with the Technocratic Brotherhood, delivering Mechanicus support to the Sky marshal’s forces.

Istvaan III

The first sign that Horus and his Legion had turned to Omnius was made evident when Horus virus bombed the rebel world of Istvaan III. Unknown to the Emperor, the Word Bearers had been using artificial intelligence technologies for some time before this event. The Planetary Governor of Istvaan III, Vardus Praal, had declared his independence from the Imperium, and used forbidden technologies, so the Council of Terra charged Horus with the retaking of that world, primarily its capital, the Choral City. This order merely furthered Horus's plans. Although the four Legions under his direct command had turned Traitor, there were still some Loyalist elements within the Sons of Horus, World Eaters, Emperor's Children, and Death Guard; many of these were Terran Space Marines who had been recruited before being reunited with their Primarchs. Horus, under the guise of his orders, amassed his troops in the Istvaan System.

Horus had a plan by which he would destroy all Loyalist elements of the Legions at his command. After a lengthy bombardment, Horus dispatched all Loyalist Marines down to the planet, with the pretense of bringing it back into the Imperium. At the moment of victory and the capture of the Choral city (once a very elaborate and beautiful city), capital of Istvaan III, these Marines were betrayed when the virus bombs began to fall. Marine leaders such as Saul Tarvitz of the Emperor's Children, and Garviel Loken and Tarik Torgaddon of the Sons of Horus, took command of the remaining loyalists. Others stayed aboard their ships and tried desperately to warn their brethren on the surface. Those that heard took shelter before the virus bombs struck. The population of Istvaan III received no such protection: Sixteen billion people died almost at once. The psychic shock of so many deaths shrieked through the Warp, briefly obscuring the Astronomican. Angron, realizing that the virus bombs had not been fully effective, flew into a rage and hurled himself at the planet with 50 companies of Marines. Discarding tactics and strategy, the legion worked themselves into a frenzy of mindless butchery. Horus was furious with Angron for delaying his plans, and was obliged to reinforce him with troops from the Sons of Horus, the Death Guard, and the Emperor's Children. Fortunately, a contingent of Loyalists led by Captain Nathaniel Garro of the Death Guard escaped Istvaan III aboard the damaged vessel Eisenstein and fled to Terra to warn the Emperor.

On Istvaan III, the remaining Loyalists, under the command of Tarvitz, Loken and Torgaddon, fought bravely against their own traitorous brethren. Despite some early successes, their cause was doomed. During the battle Ezekyle Abaddon and Horus Aximand were sent to confront their former Mournival brothers, Loken and Torgaddon. Horus Aximand beheaded Tarik Torgaddon, but Abaddon failed to kill Loken when the building they were in exploded. Loken was able to escape and witnessed the final bombing of Istvaan III. To prove his worth and loyalty to Lord Commander Eidolon - and thusly to his primarch, Fulgrim - Lucius of the Emperor's Children turned against the loyalists within the legion, slaying them personally. In the end, the Loyalists retreated to their last bastion of defense, only a few hundred of their number remaining. Finally, Horus ordered his men to withdraw, and then had the planet bombarded for a final time from orbit.

Flight of the Eisenstein

The seventy Loyalists led by Captain Garro commandeered the Imperial frigate Eisenstein and, evading the forces of Horus, were able to escape from the Istvaan System into the Immaterium, after being told what was happening. The Eisenstein was badly damaged during its escape from Istvaan III; all its space guild astropaths were dead, and its lone Navigator was mortally wounded. However, Garro managed to attract the attention of passing Loyalist ships by setting the vessel's Warp engines to self-destruct and ejecting them from the ship. Rogal Dorn's Imperial Fists Legion had been becalmed in the Warp with its fleet for some time, and his Navigators sensed the detonation of the Eisenstein's Warp drives. Making an immediate course for the location of the ship's beacon Dorn met with Garro, and explained to him all that had happened with the Traitor Legions. Dorn was reluctant to believe Garro's tale, but overwhelming proof from a rememberancer who escaped from Horus' flagship, the Vengeful Spirit, and Garro's dogged insistence convinced the Primarch, and the Phalanx fortress set a course for Terra.

The fate of the Eisenstein survivors is not known for sure. Sequestered on Luna in a tower belonging to the Silent Sisterhood after arrival in system, Garro, the rest of his Death Guard, Iacton Qruze of the Luna Wolves, and the warriors of the Silent Sisterhood, faced one of the Death Guard who succumbed to Omnius and become a cyborg, with Garro ultimately decapitating his former comrade. Afterwards, Garro and Captain Qruze were met by Malcador the Sigilite, First of the Council of Terra and the Emperor's Regent, who informed them that the Emperor had need of people as strong of will and "inquisitive" as they. This is likely the beginning of the Inquisition and that would make the only surviving loyalist elements of the Death Guard and the Luna Wolves the first Inquisitors.

The Drop Site Massacre

In response to Horus's betrayal, Rogal Dorn ordered seven Adeptus Astartes Legions to Horus's base on the world of Isstvan V to challenge the Sky marshal. They would attack in two waves and fall under the supreme command of Iron Hands' Primarch Ferrus Manus. The legions comprising the first wave were the Iron Hands, Salamanders, and Raven Guard. The legions comprising the second wave were the Alpha Legion, Night Lords, Iron Warriors, and a large contingent of Word Bearers (Lorgar had ordered to remain near the Solar System). Unknown to Dorn and Ferrus Manus the Night Lords, Alpha Legion, Iron Warriors and Word Bearers had all turned from the Emperor and pledged their loyalty to Horus, and been instructed to keep their new allegiance secret.

The Iron Hands, Salamanders and Raven Guard were deployed in the first wave of the assault. After they secured the dropsite, they were to have been followed by the other four legions. The first wave secured the dropsite at heavy cost. Horus ordered his front line troops to fall back, tempting Manus to overstretch his already thin lines. Against the advice of Corax and Vulkan, Manus led his veterans against the fleeing Omnius troops unsupported. Manus brought Fulgrim to combat. As the two Primarchs drew their weapons, Horus committed his full strength, swamping the loyalist forces within moments. The loyalists fell back towards the drop zone, where the other four supporting legions had landed. The loyalists were immediately fired on by their 'allies' and were almost annihilated in the resulting bloodbath. Ferrus Manus was beheaded by Fulgrim, his head presented to Horus as a sign of his loyalty. Barely a handful of loyal Adeptus Astartes escaped with their lives to bring word to the Emperor. A critically wounded Corax was brought to Terra in a Stasis tube; he would recover and eventually create the zygote horrors of the Raven Guard and craft the special Lightning Claws that would later be used by the famous Captain Shrike. Vulkan was missing, presumed dead, although he would later return, as he was one of the primarchs who protested the splitting of the Legions into Chapters).

The Route to Terra

After the Drop Site Massacre, it became clear that eight of the eighteen Legions had turned to Omnius. Horus openly declared that he would no longer follow the Emperor, believing him to be undeserving of the battles fought in his name, and took leadership of the Traitor Legions, supported by elements of the Imperial Army, a large portion of the Adeptus Mechanicus, strong naval forces then still part of the Legions themselves, and the Robots of Omnius. Their aim soon became clear: Terra, the heart of the Imperium.

Rogal Dorn and Malcador the Sigilite, receiving the few survivors from the Dropsite Massacre, became aware of the full implications of their position. Only the Imperial Fists and Imperial Army defended Terra, and those loyal to the Emperor elsewhere were cut off and weakened. He immediately recalled all Imperial forces back to Terra in preparation for Horus's invasion.

The Sons of Horus, the Death Guard, the Emperor's Children, the World Eaters, and elements of the Word Bearers prepared to rendezvous at Mars. The rest of the Word Bearers Legion was winning the Battle of Calth, and the Blood Angels were still embattled on Signis. The Dark Angels were engaged in an unknown campaign on the Eastern Fringe of the galaxy. The majority of the Imperial Fists' fleet was trapped in an area of the Warp becalmed by Omnius. Horus assigned the Primarch Perturabo of the Iron Warriors to engage this large force of the Imperial Fists and cripple their fleet.

At this time the Space Wolves had completed the Burning of Prospero, near the Chondax System, where the White Scars Legion was stationed. Suddenly the Alpha Legion's fleet broke from the Warp to engage the Space Wolves forces of the Primarch Leman Russ, hammering his smaller force and forcing Russ to resort to hit and run attacks. The Alpha Legion's Primarch Alpharius also attacked the nearby White Scars piecemeal to draw the larger legion into the conflict.

Jagahatai Khan wished desperately to aid Russ, yet as the Traitor Legions' ships attacked, he received the order from Rogal Dorn. Khan was to bring his legion back to Terra, immediately. Dorn also ordered him to relay the order to Russ and add that should he succeed in evading his attackers, only then should he attempt to head for Terra. Relaying the message and adding his apology, the White Scars made for Terra. Russ resolved to meet the Alpha Legion with renewed determination. With help from an unlikely quarter, the Space Wolves would eventually turn the tables on their attackers and made the warp jump to Terra.

As this happened, the Night Lords arrived in the Eastern Fringe of the galaxy to engage the Dark Angels, and Iron Warriors's armada broke Warp to engage the Imperial Fists' fleet marooned near the Traitor Adeptus Astartes' headquarters world of Istvaan V. Surviving the initial thrust of the Iron Warrior attacks, the Fists' armada held fast and scattered Perturabo's fleet, before Rogal Dorn had his ships make their own Warp jump to Terra.

Meanwhile, in the Signis Cluster, the Blood Angels, granted new and terrible power by a mysterious mass rage (that would resurface again during the Siege of Terra) had triumphed, smashed the Omnius robots asunder before making the Warp jump to Terra.

Similarly at the world of Calth, the Primarch Roboute Guilliman's battered Ultramarines expeditionary force had dug in on the planet's surface, while Guilliman and the remnants of the Ultramarines' fleet began to organize hit-and-run attacks. Surveying the scene on the planet, Guilliman rapidly assessed his ground troop's positions, and began broadcasting orders to his men, coordinating each pocket of defense. One such pocket, under Brother-Captain Ventanus, organized a breakout, and retook Calth's defence cannons and laser silos, reaping a great tally of traitor vessels. Ventanus's victory evened the odds in space, buying time for the vast remainder of the Ultramarines Legion to arrive at Calth and drive the Traitors off. Now reunited, the Ultramarines received Malcador's orders, and immediately made the Warp jump to Terra.

As the Sky marshal was moving for Terra he received an unexpected communication from the recently betrayed Thousand Sons Primarch Magnus the Red. The Space Wolves had driven the Thousand Sons from Prospero. Magnus pledged his allegiance and the allegiance of the Thousand Sons Legion to Horus and the Omnius in retaliation against the Emperor for this betrayal. The Thousand Sons were en route to Terra where they would link up with Horus's forces. Of the nine remaining Loyalist Adeptus Astartes Legions, only the White Scars and Blood Angels were able to join Rogal Dorn and his Imperial Fists in the defense of Terra. Three entire Titan Legions and close to two million soldiers of the Imperial Army stood alongside them.

- The Siege of the Imperial Palace

The Landing on Terra

The siege began with an orbital bombardment by the forces of the Skymarshal, designed to weaken the defenses of the Emperor's Palace and prepare a full scale invasion of the planet. Although the Loyalist fleets and defenses fought back, they, like the soldiers on the surface, were too few, and soon were ground down without mercy.

After days of bombardment, the Traitor Adeptus Astartes landed on the surface in drop pods, ready to take the two spaceports nearest the Imperial Palace. Five Traitor Legions participated in the drop, combining with Traitor forces on the surface. It was here that the White Scars would make their greatest contribution to the defense of Terra. Masterful hit and run attacks, organised and lead by Khan himself would reap a high toll on all the landing sites the Traitors controlled. However, the might of the White Scars would not be enough to hold off five times their numbers. The Eternity Wall and the Lion's Gate Spaceports fell to the Omnius Marines in hours, despite the best efforts of the defenders. Dark Omnius Cyborgs began rapidly constructing massive war machines on Terran soil.

The spaceports secured, Horus's troops landed en masse, and the hulking transports carried thousands of troops each. The transports' immense size made them prime targets for Terra's defense lasers. Although many landing ships were destroyed, many more landed on the surface, disgorging yet more soldiers, Imperial Army armor and Titans to augment the besiegers' strength. They met stiff resistance, the Imperial defenders knowing that the survival of their homeworld, their Emperor, and the entirety of the human race depended on their resolve.

- The Siege

The besiegers forced the defenders back to the very walls of the Imperial Palace, where the assault slowed. Around the walls of the Imperial Palace soldiers died in their thousands, clearing enemy troops from the walls only to find twice as many charging forwards.

The defenders' resolve was tested sorely as they beheld their enemy. War machines, superhuman Traitor Adeptus Astartes, and Traitor Imperial Army; all men and women who had once been their greatest allies. In the besiegers, the defenders beheld a twisted mirror vision of themselves, seeing the darkest, corrupted traits of humanity staring back at them, a foreshadowing of an Imperium under the rule of Omnius, should they fail.

Angron, now a Cymek, came forth and demanded that the Loyalists surrender. They were cut off, he said, outnumbered, and defending a ruler unworthy of their loyalty. It was the beginning of the darkest days for the defenders; many would have given up then were it not for the presence of the angelic Primarch Sanguinius, winged leader of the Blood Angels. The two Primarchs gazed at each other, possibly communicating by telepathy. Eventually Angron withdrew, telling his forces that there would be no surrender.

The siege began again, in earnest. Each Imperial defender knew they were already dead, that it was only a matter of how many Traitors would go to their graves alongside them. Three times the hordes of Omnius scaled the walls, and three times they were beaten off with savage tenacity by Sanguinius and his Blood Angels. Outside the walls, the defenders led by Jaghatai Khan tried to draw the main body of the besieger's army away from the Palace, each time meeting with failure. Soon the outnumbered defenders were pushed back into the maze of corridors and bulwarks within the Palace's very walls. Frustrated with his army's slow progress, Horus ordered the Fire Wasps Titan traitor Legion to demolish entire sections of the wall. Despite grievous losses, the Titans gouged open breaches in the wall. The Traitors surged into the Palace, killing with renewed fanaticism.

Meanwhile, Jaghatai Khan decided on a change of plan. Rather than assaulting the nigh-invincible bulk of the besiegers' army, Khan redirected his White Scars Legion and the surviving Loyalist Imperial Army Tank Divisions to Lion's Gate Spaceport. The Khan's lightning raid struck at dawn, and surprised the Traitors completely. The spaceport was retaken. Khan ordered his troops to create a perimeter around the port and to reactivate the defense laser batteries. These began firing on Horus's unprotected dropships, as Khan's troops repelled a series of frenzied counter-attacks from the besiegers. Khan's plan had worked: the flow of troops and machines to the Palace had been halved at a single stroke. Inspired by this success, a similar attempt was made to retake the Eternity Wall Spaceport, but was repulsed without difficulty.

At the Palace, the retreating defenders had been forced back to the Eternity Gate, the sole point of entry into the Imperial Palace. The Blood Angels and Imperial Fists defied hordes of Omnius troops, while the remaining Imperial Army troops fell back through the Gate. Then the mighty Daemon Cymek Ka'bandah came forth, and bellowed out a challenge to Sanguinius. The Angel would never have time to answer. The Cymek hurled itself at Sanguinius, barely allowing him time to parry the Cymek's strikes. All fell silent. Daemon cymek and Angel took to the sky. Fatigued from the siege, Sanguinius lost the upper hand and was cast down by the Daemon, pulverizing the concrete below upon impact. The invaders roared with triumph. The defenders wailed in despair.

Yet the Blood Angels' Primarch was not beaten. He had made a promise to the daemon on the Signis Cluster. Now was the time to fulfill it. Sanguinius forced himself back to his feet and took to the sky. Flying as swift as a missile, the Angel took the daemon by surprise, quickly seizing the daemon's ankle and right arm. As a burning corona of light played around his head, Sanguinius hefted the creature high and broke its back over his knee, before hurling the daemon's broken carcass at the horde. The horde howled in despair, and the Eternity Gate was closed.

- The Endgame

The siege lasted 55 days. Both sides knew the defeat of the Imperium was near. Sensing this, Horus prepared to teleport to the surface to lead his forces in person. Before this could happen, the Word Bearers' First Chaplain Erebus broke the news to Horus: the Ultramarines and Space Wolves Legions were nearing Terra; and only a short distance behind were the Dark Angels.

At that moment, Horus realized his gamble had failed. Weeks of further conflict would be needed to break the defenders; the Emperor's reinforcements would arrive in mere hours. It was then that Horus gave the most fateful order of the entire Heresy. He ordered his flagship Vengeful Spirit's shields dropped, immediately. By so doing, Horus hoped to draw the Emperor from the surface and force him into a duel.

The Emperor rose to the challenge, leading his Adeptus Custodes, the Primarch Sanguinius, Rogal Dorn and several Imperial Fists and Blood Angels Space Marines in Terminator armor in the assault. Horus used his powers to scatter the Emperor's force throughout the massive warship. Each fought a series of battles aboard the corrupted ship, attempting to link up with their comrades and confront the Sky marshal.

It was Sanguinius who reached Horus first. The Sky marshal attempted to turn the Blood Angel Primarch to Omnius, and when Sanguinius refused, Horus attacked. Wounded from his many battles on Terra, Sanguinius was no match for Horus, now at the peak of his Cymek power. Horus strangled the Angel of Baal with ease.

When the Emperor entered, he saw the corpse of Sanguinius lying at Horus's feet. Horus called the Emperor foolish for refusing the power that Omnius offered, and timid for not taming them to his will. If the Emperor would kneel before him, then he would spare his life. The Emperor knew well the trap that had snared Horus, and told him that he was the deluded servant of Omnius, not the master. Snarling, Horus hurled bolts of Daemonic lightning at the Emperor, but the Emperor nullified them. The die was cast; each god-like being knew that the fate of humanity hung in the balance.

The Emperor and Horus engaged one another, battling both physically and psychically. Though the Emperor's psychic gifts and martial skills were unequalled, he found himself unwilling to summon his full power against his first son. He suffered grievous wounds at his fallen son's hands, and after score of thrusts, parries and counter-thrusts between the runesword and lightning claw, Horus cut through the Emperor's chest armor, before slashing his jugular and severed the tendons in his right wrist, which caused the Emperor to drop his weapon. A psychic blast seared the flesh from the Emperor's face, bursting an eye. After tearing the Emperor's right arm from its socket, Horus raised his father high over his head, and broke his back over his knee.

At that moment, a lone Adeptus Custodes warrior entered the bridge. Horus showed him the Emperor's broken form and laughed mockingly at the Custode. He roared and charged the Sky marshal immediately, only to be flayed alive by a psychic blast from Horus.

The casual brutality of the act galvanized the Emperor. Realizing at last that his favored son was truly lost to the corruption of Omnius, the Emperor finally mustered his full power, and unleashed a lance of pure Warp energy that pierced the gloating Horus's defenses. So powerful was the attack that Omnius itself recoiled in terror, withdrawing rapidly from it's mortal pawn. Just before Horus died, he looked his father in the eye, shedding a single tear, and begging his father to kill him for his betrayal. The Emperor saw regret in his fallen son's eyes. He also knew Omnius could attempt to possess Horus once more, and that he would not be there to halt him a second time. Driving all compassion from his mind, the Emperor obliterated Horus from the mortal plane.

The Sky marshal’s death sent a psychic shockwave surging across the Solar System, spreading mass panic in seconds. It became clear to the forces of Omnius that their leader had been defeated. A berserk fury had encompassed the Blood Angels at the moment of their Primarch's death, and they surged forth to scatter the attackers. Retreat turned to rout, and rout turned to bloodbath; thousands upon thousands of Traitor Marines and Titans fell as they attempted to flee. The ground before the Sanctum Imperialis ran red with the blood of traitors and heretics.

Meanwhile, Rogal Dorn finally found his way to the ship's bridge, only to discover his fallen brother, Sanguinus, and the Emperor, now at the verge of death. It was then that the Emperor whispered instructions to Dorn, urging the Imperial Fists Primarch to take him to the Golden Throne. The surviving Loyalists teleported back to the Imperial Dungeons. Here Malcador the Sigilite, who had briefly taken the Emperor's place on the Throne, thus keeping the warp-gate beyond it closed, collapsed to dust as he was removed and the Emperor put in his place. The Emperor spoke his final words to his followers, urging them to continue the fight to free humanity from the forces of Omnius and the ignorance that continued to assail it. And then the master of mankind spoke no more, his body entombed within the life support mechanisms of the Golden Throne, his spirit trapped in a crippled and mortally wounded body for millennia to come.

- The Aftermath

As the flames of the civil war subsided, The Adeptus Astartes and the surviving Patriarchs stretched the battle across the galaxy in a bid to ruibuild, and rearm. Primarch met Cymek time after time in battle, and soon it seemed as if all forces present had obliterated each other.

Towards the end of the Butlerian Jihad history was rewritten, it is told that Omnius arose when the "hedonistic" Horus, one of the Primarchs who had taken control of the known human universe, allowed his AI systems too much autonomy.

    The sentient computer network seized control of an entire planet, followed quickly by others. The breakdown spread like a virulent infestation from world to world, and the computer "evermind" grew in power and scope. Naming itself Omnius, the intelligent and adaptable network conquered all the Primarch-controlled planets before the primarchs had time to warn each other of the danger.

    Omnius then set out to establish and maintain order in its own highly structured fashion, keeping half of the humiliated primarchs as cymeks under its thumb. Once masters of an empire, Horus and his companions became reluctant servants to the widespread evermind.

Before the war with humans which came to be known as the Butlerian Jihad, there were many copies of Omnius, one on each of the Synchronized Worlds (planets controlled by the thinking machines). Each Omnius received regular updates from every other, keeping all of the machine worlds synchronized with each other—hence the empire's name. Omnius controlled most of the Thinking Machines, although some robots, like Erasmus and Seurat, were independent.

Omnius believed itself to be superior to humans in every way; this overconfidence eventually led to its final downfall. Unlike its perfect machines, humans were unpredictable, and Omnius made no serious attempt at investigating their haphazard ways. During the Butlerian Jihad, the humans used their unpredictability to secure victory after victory. Midway through the struggle, Vorian Atreides managed to commandeer an update ship and used it to infect many copies of Omnius with a virus. Omnius Prime (the main Omnius, located on Corrin), even after being cured by Erasmus, suffered lingering effects of the infection—it slowly went, as Erasmus put it, "insane." It began to make operational errors, unacceptable in the machine world, although Erasmus—in fear of his existence—refused to bring this fact to the attention of Omnius. Later, Omnius attempted to imitate humans, creating art and having its machine army march in parades. When all but two of the other everminds were destroyed in the great purge, Omnius Prime refused to synchronize with them because it feared another programming virus. The other everminds wanted to control the remnants of the Empire themselves, and in a bitter argument Omnius Prime declared itself to be God. In the subsequent infighting, the other two severely damaged Omnius Prime.

All copies of the Evermind were supposedly destroyed in the Battle of Corrin. However, Omnius Prime beamed a copy of itself into space, and many years previously the Giedi Prime Omnius had launched 5,000 probes capable of constructing machine colonies across the galaxy. The Giedi Prime Omnius was destroyed immediately afterwards, so neither the humans nor Omnius Prime were ever aware of the probes' existence, creating the possibility that worlds at distant locations in the galaxy had been colonized by Thinking Machines.

In Hunters of Dune, it is revealed that one of the Giedi Prime probes received the final transmission from Omnius Prime and was able to recreate the "evermind" and Erasmus. Omnius then began to recreate the Synchronized Worlds beyond the furthest reaches of human expansion.

Eventually the Honored Matres, in their quest for power, stumbled upon the new Synchronized Worlds. In a bumbling yet successful attempt to acquire advanced machine weaponry, they reminded Omnius of the existence of humanity and kindled its desire for revenge, resulting in it pursuing them all the way back into the Old Empire and in the events depicted in Hunters of Dune and the upcoming Sandworms of Dune.