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History
The Blood Shepards do not fit the standard template of Excommunicate Traitoris. Unlike most Renegade chapters which have devoted themselves to the Chaos gods, the Blood Shepards despise the Ruinous Powers as much if not more than they hate the Imperium that cast them out. Instead, they have developed an ideology that states that the Imperium has betrayed everything the Emperor has stood for; so they still fight the powers of chaos even though they disagree with what the Imperium now stands for. Some within the Chapter think that the Imperium should be destroyed for the good of mankind.
It began with an operation to obtain one of the Chapter's lost relics, the great Soulsword, a weapon used by Allister Khaine during the Great Crusade, from a criminal organization that had come to possess it. Just as the 800 Blood Shepards had taken the orbital defense platform where the relic was being held, and were about to reclaim the Sword, supporting Adeptus Mechanicus forces teleported into the vault it was stored in and made off with the Sword before the Blood Shepards could react. The Blood Shepards then fortified the platform and demanded the return of their relic, but it had already been passed along to another vessel that was en route to a Forge World. The Mechanicus then revealed a great siege cannon from their starship, and forced the Blood Shepards to board and destroy the Mechanicus weapon before it could be used against them, slaying thousands of Tech-Guard in the process before fleeing aboard their two Strike Cruisers.
The Inquisition, caring not for the reasons why, saw only that the Blood Shepards had attacked another Imperial institution and demanded they surrender themselves. After Sarpedon's refusal, the entire Chapter was declared Excommunicate Traitoris. Soon after, the rest of the Blood Shepards and their fleet arrived to extract the two beleaguered Cruisers that they might answer for their actions to the Chapter Master, Gorgoleon.

1st Chapter War
Gorgoleon was obstinate, and saw the Blood Shepards of Allister Khaine at fault, and fought him for the fate of the Chapter. Allister Khaine emerged victorious, sparking a war within the Chapter. Most of the Novices refused to follow Allister Khaine, and took up arms and barricaded themselves throughout the fleet. It took Allister Khaine and his forces, who counted most of the Chapter's specialists amongst them, several months to root them out and kill them all.

Under the Sway of a Daemon Prince
Disillusioned by the Imperium, and unknowingly under the influence of a Khorne Daemon Prince in the desguise of an aspect of the Emperor, Allister Khaine opted to keep his Chapter renegade, scuttled the Blood Shepard fleet, and resettled the Chapter into a Space Hulk they dubbed Destinys Assention. Soon after, the Daemon Prince Abraxes mislead the Blood Shepards into attacking one of his rivals, the Nurgle Daemon Prince Ve'Meth. After slaying Ve'Meth, who took the form of a virus infesting several hundred ordinary people, Abraxes revealed his true nature. He handed Allister Khaine the Soulsword and offered the Blood Shepards the chance to serve as his personal retinue of Chaos Space Marines. Though Allister Khaine considered his options, he accepted the offer, secretly plotting to turn on the daemon prince.

The Empire of Teturact
The heretic Teturact, a life-form produced by Adeptus Mechanicus experiments in Human mutations on desolate Stratix Luminae, was carving a vast empire out of the Imperium of Man. His ability to project noxious, mind-controlling viruses and even raise the dead with them won him godhood in the eyes of those he infected. He was able to claim several important Imperial worlds, including the Hives of Stratix, the Forge World Salshan Anterior, and several others including agri-worlds and other strategic targets. One of these worlds was Stratix Luminae, a world where the old Blood Shepards had once fought, granting Allister Khaine a knowledge of the experiments carried out there. The Blood Shepards sought out the surviving Mechanicus personnel from Stratix Luminae across several of the worlds under Teturact's sway, all the while dodging the efforts of the Inquisitorial Taskforce Thaddeus to track them down and bring them to justice, before finally collecting all the pieces of the puzzle that sent them to Stratix Luminae itself. Teturact intervened personally, intentionally breaking up his flag-battleship in orbit to rain debris and his followers down on the Blood Shepards.

Dealing with Tellos
After the defeat of the heretic Teturact, the Blood Shepards were forced to flee Stratix Luminae, leaving several assault squads, who were under Tellos' command, behind.
Chapter Master Allister Khaine quickly caught wind of this heresy by his battle-brother and tracked Tellos to Entymion IV, an Imperial world held by a mysterious alliance of Dark Eldar and Slaaneshi Cultists. The Imperial Guard, with the assistance of the Crimson Fists, were at that moment trying to liberate the world.
The Crimson Fists force was initially small, serving as a spearhead for the array of Imperial Guard regiments attempting to retake the capital city of Gravenhold. However, they quickly fell afoul of Tellos' Blood Shepards, clashing indecisively as the Fists took up overwatch positions in a cathedral. In the aftermath, recognizing the chalice emblem and believing the entire Blood Shepards Chapter present, Crimson Fists Commander Reinez sent word of the Blood Shepards presence to Rynn's World, who responded with the Fists 2nd Company under Chaplain Inhuaca, placing himself and the Company under Reinez's command with orders to destroy the Blood Shepards and bring back Chief Librarian Allister Khaine's head.
Upon their arrival on Entymion IV, Allister Khaine's Blood Shepards immediately began investigating the situation. Their method of infiltrating the world, hijacking a pair of landers from the Imperial Navy, quickly alerted the Crimson Fists as to their location. After securing the assistance of the Armoured Fist units of the Fornux Lix Fire Drakes Regiment, the Crimson Fists dove deep into the city and fought the Blood Shepards in a brutal brawl within the city's Mercantile Chamber. The Blood Shepards pulled back after capturing the Fists Company Standard and killing the company Librarian.
Throughout this fight, the Dark Eldar present on the world observed the Blood Shepards fighting against the loyalist forces. The intervention of the brainwashed slave army of the Dark Eldar deterred Fists pursuit as the Blood Shepards retreated beneath the city. They were quickly approached by the Dark Eldar- who, clearly bearing betrayal in mind - offered Allister an Alliance, which Allister- also planning betrayal - accepted.
Interested in nothing save finding Tellos, Allister split the Blood Shepards into two parts to blunt the Imperial Guard for the Dark Eldar, all the while the Blood Shepards Scouts sought out Tellos in the city. The Scouts soon located Tellos and his retinue as they butchered through a Guard regiment, and Chaplain Iktinos and his flock were able to hold them in place long enough for Allister to arrive and defeat Tellos, collapsing a span bridge on top of him. The Dark Eldar still benefited from this, buying time for a secret army of mutated human slaves to fully awaken beneath the city and begin a slaughter so great it would propel Entymion IV to the status of Daemon World, one ruled by the Dark Eldar as a second Commorragh. The Blood Shepards would ultimately have the last laugh, using their Scouts to trick the Crimson Fists into attacking the Dark Eldar stronghold on the world, slaying all the xenos and preventing their plan from reaching fruition. Though prematurely stopped, the hole in reality leading into the Warp tainted the world beyond hope, and the whole world was destroyed by Exterminatus.

2nd Chapter War
The Blood Shepards found another Chapter War brewing between Allister, and the new Sergent Eumenes, taken from a planet that hated the Imperium, to restock the Chapter. Eumenes felt that the fight should be taken directly to the Emperor. He wanted to take out the Astronomican, and blot out the light that guides the Emperor's ships through the warp to start the Imperium over.Allister, however, struck a new course for the Chapter after being given advice from Chaplain Iktinos that a planet called Vanqualis was under attack from a horde of Orks and needed their protection. Afterwords, the Blood Shepards would be able to benefit by taking on supplies for their new home, Destinys Assention. Allister led the Blood Shepards through the jungles of Vanqualis to battle the Orks, but in his absence Eumenes took control of Destinys Assention and started a coup that included a great deal of the forces on the planet. After consolidating, Allisters Blood Shepards set out to take an old fortress from the rebels. Once there, Librarian Gresk warned Allister to leave. He did, before Eumenes bombarded the land surrounding the fortress from Destinys Assention.
The Howling Griffons Chapter had sent three Companies under Lord-Librarian Mercaeno to the world to honor an old debt the Chapter owed Vanqualis. The Griffons had also allowed Inquisitor Thaddeus, now disfavored within the Inquisition, to tag along on the suspicions of the Blood Shepards involvement. Though he realized that Mercaeno didn't comprehend what the Blood Shepards really were, he could not convince him of this fact. Thaddeus tried to leave the Strike Cruiser and warn Allister of the Griffons, but had to kill one of the Griffins in a close-quarters firefight before he could escape. Mercaeno and his Griffons landed shortly thereafter, and did battle with Allisters group while the traitors watched bemusedly from the sidelines. It was during this that Mercaeno killed Thaddeus for killing his battle-brother.

Aftermath
Allister could not get off Vanqualis, and conceded to Eumenes' wishes. Eumenes became the new Chapter Master. Allister led the loyal Blood Shepards to Techmarine Lygris, loyal to Allister, but was stuck on Destinys Assention until Eumenes let him shuttle Allister and his forces back to their ship in time to repel a boarding attack from the Howling Griffins. Allister and Mercaeno engaged in a titanic psychic duel, tiring each other out until Eumenes struck down Mercaeno from behind and throwing Allister in the brig. Allister then attacked psyker-latent Scout Scamandar in Destiny Assention’s brig, incapacitating him. Allister then made his way to the bridge, where he dueled Eumenes. Though Eumenes had both the Soulsword Mercaeno's force axe, Allister impaled him and won the battle.

Necrons
While fleeing from a Adeptus Mechanicus task force, the Blood Shepards Space Hulk was severely damaged and low on fuel. Forced to run, the Blood Shepards went deep into the veiled regions in search of fuel. They ran into the Necrons on many worlds, all with signs of previous human settlement, but now infested with the undying xenos. Eventually they discovered the last of the human worlds that the Necrons were still in the process of cleansing, and the Blood Shepards made a deal with the survivors. They allowed the human's time to retreat to their space-craft while they held the Necron forces off, in exchange for the Blood Shepards receiving fuel.
The Blood Shepards held out aganist the Necrons, and the human population reached their spaceport but a Necron fleet arrived in-system, preventing them from leaving. The Adeptus Mechanicus fleet arrived shortly after, and the two fleets began fighting against each other. It was immediately obvious that the imperial forces would be destroyed, so they began a complex pattern of manoeuvers to delay the inevitable.
When the Blood Shepards realized they could not beat the approaching Necron force on the ground, and the Mechanicus would lose in space, Allister offered an alliance with the Mechanicus. Chaplain Iktinos and his "flock" remained behind to help defend the spaceport and the surviving humans. It was revealed that his "flock" was loyal to his secret master as well, and no longer considered themselves Blood Shepards.
Accepting the alliance the Mechanicus and Blood Shepards set off for the main Necron hub, planning to destroy the Necron Lord and leave the rest of the enemy forces leaderless.
Arriving at the Tomb World, the Mechanicus crashed their ship into the planet and deployed alongside the Blood Shepards. A long bloody battle began as they raced to kill the Necron lord, before the Necrons superior numbers began to change the odds. Finally they arrived at the Necron Lord's location and Allister duelled with it and won. However in typical Necron fashion it got back up, and began crushing him to death. Only by the sacrifice of Techmarine Lygis was the lord defeated.
Gathering his forces Allister lead his remaining troops towards the crashed Adeptus Mechanicus ship, where their promised transports were to be awaiting them. Instead three Imperial Fists thunderhawk gunships deployed upon the surface, while twenty terminator armoured elites teleported onto the planet, lead by First Captain Lysander. He ordered the Blood Shepards to surrender or be destroyed. Allied replied with the challenge of a personal duel. Allister defeated Lysander but did not kill him. He left with his men, victorious.

Oh look, the Soul Drinkers have had a makeover!