Second Imperial Civil War

"[...] join with me and take back our Empire which you have so long and faithfully served."

- Emperor Roan Fel

The Second Imperial Civil War, also known as simply the Imperial Civil War and to the Galactic Alliance Core Fleet as the Second Rebellion, was a conflict that began with the end of the Sith–Imperial War in 130 ABY. It was the result of the Imperial victory at Caamas, in which part of the Galactic Alliance Defense Fleet refused to surrender; the Massacre at Ossus took place, in which several Jedi managed to survive; and, finally, the coup executed by Darth Krayt and the One Sith. This resulted in the fragmentation of the Fel Empire into two factions, one loyal to Fel and another loyal to the Dark Lord of the Sith. Over the next seven years, Krayt's empire was challenged by both Fel's Imperial supporters and the remnants of the Galactic Alliance under Admiral Gar Stazi.

By 137 ABY the insurgency was still ongoing and was accelerated by Fel's capture of the Outer Rim Imperial fortress world of Bastion, providing Fel's forces with a staging center to coordinate the war against Krayt's Empire. Following the Battle of Dac and Krayt's genocidal campaign against the Mon Calamari species, Fel's Imperial faction aligned itself with the Stazi's Galactic Alliance Remnant despite earlier Sith attempts to sabotage negotiation efforts. Both forces cooperated in several key campaigns including a raid on Ralltiir and the Evacuation of Dac.

A unexpected albeit secret development in the war occurred when Darth Krayt was killed by his most trusted adviser Darth Wyyrlok III after a duel with the Jedi on Had Abbadon. Alleging that Krayt was ill and had entered into seclusion, Wyyrlok III took de-facto control of the Empire while claim to rule on his master's behalf. However, Krayt was resurrected through the dark side of the Force and revealed himself to members of the One Sith before unleashing his secret weapons on all his opponents including Fel's Imperial loyalists, the Alliance Remnant and the traitarous Wyyrlok.

A fourth faction within the conflict was composed by the surviving members of the New Jedi Order, such as Wolf Sazen, Shado Vao and K'Kruhk, with the support of Master Shaper Nei Rin, who also sought to work with Fel and Stazi in order to bring down the Sith and reestablish their place in the galaxy.

Origins
"The true Roan Fel knew we were coming. He smelled a trap and has now escaped."

- Darth Krayt, to Darth Maladi



The Second Imperial Civil War was the result of a successful coup in 130 ABY by Darth Krayt's One Sith which overthrew Roan Fel&mdash;ruler of the Galactic Empire and a leader of the light side Imperial Knights. Prior to the coup, most of the Galactic Alliance had capitulated with the exception of Admiral Gar Stazi's Core Forces following the Battle of Caamas. Following the victory, the Sith attempted to destroy the Jedi Order by attacking the Jedi Academy on Ossus, against the express orders of Emperor Roan Fel. The Sith coup was secretly backed by a number of prominent members of the Imperial Moff Council including Grand Admiral Morlish Veed and Moff Nyna Calixte. However, Moff Calixte realized that with Fel gone, the Sith would no longer need the Moff's Council to control the Empire. Thus, she warned Fel of the impending coup, allowing him to replace himself with a double while escaping offworld. The coup established Darth Krayt as Galactic Emperor over much of Fel's Empire despite resistance from Fel loyalists and the Alliance Remnant.

Fel's Imperialists loyalists included the Imperial Knights, the 501st Legion , the 908th Stormtrooper Division and the Bastion Second Fleet. On the other side were the Imperials who believed in loyalty to the institution above the individual and therefore had sided with Krayt's One Sith, including the 407th Stormtrooper Division, the Outer Rim Third Fleet , the Coruscant Third Fleet and the Moff Council, though the Council sought to undermine the Sith's efforts in order to achieve its own ambitions. Krayt controlled much of the galaxy including key centers like Coruscant, Ralltiir and Dac. Meanwhile, Stazi's Core Forces had evolved into the larger Galactic Alliance Remnant which fought Darth Krayt's Galactic Empire. Over the next seven years, Krayt's empire was challenged by both factions.

The Alliance Remnant was composed of surviving remnants of the Core Fleet and other Alliance units. In addition to numerous battle cruisers and escort vessels, Stazi's fleet also included one of the elite starfighter units&mdash;Rogue Squadron led by Weequay Commander Jhoram Bey. The Mon Calamari, longtime supporters of the GA and its Rebel Alliance and New Republic predecessors, supplied Stazi with spare parts, supplies, bacta, and new recruits. This helped to keep Stazi's fleet combat-ready, though supplies were increasingly hard to come by, due to similar actions undertaken by Roan Fel's Loyalist forces.

A fourth faction within the conflict was composed by the surviving members of the New Jedi Order, such as Wolf Sazen, Shado Vao and K'Kruhk, with the support of the Yuuzhan Vong Master Shaper Nei Rin, who also sought to work with Fel in order to bring down the Sith and reestablish their place in the Galaxy.

Recapturing Bastion
"I'm not here to surrender. I am here to take possession of Bastion in the name of the Imperial Throne. My Throne."

- Emperor Roan Fel



After seven years of guerrilla warfare against Krayt’s Empire, Fel moved to retake Bastion, the former capital of the Imperial Remnant and an impregnable fortress world. Escorted by his Imperial Knights, the Emperor landed on Bastion where he was immediately greeted by an honor guard of the Imperial stormtroopers of the 501st Legion. Fel gave an impassioned speech to these troops, calling upon them to join him in the fight against the usurper Dark Lord of the Sith. The 501st immediately knelt before their rightful Emperor, thus leaving the service of Krayt's Empire.

An attempt by the pro-Sith Lieutenant Kiefer to arrest and subsequently assassinate Fel was thwarted by General Oron Jaeger, commanding officer of the 501st Legion. Jaeger told Fel that his forces were under Fel's command, and the takeover was complete. Thus Fel regained control of Bastion with virtually no casualties and gaining the support of the Imperial garrison. With Bastion under Imperial control, Fel moved to gather his forces against Krayt, hoping to keep his quiet takeover of Bastion a secret to the galaxy, especially to Krayt. Despite this success, meanwhile Fel’s 908th Stormtrooper Division on Borosk was wiped out by the loyalist 407th Stormtrooper Division under the command of Darth Maleval.

Hoping to draw Fel into the open, Krayt ordered his personal assassin, Darth Talon, to capture or drive Fel's daughter, Marasiah Fel, to her father. Though his daughter was on the run, Fel ordered his Imperial Knights, especially Antares Draco and Ganner Krieg, to keep away from Marasiah. Fel knew that Krayt couldn't find out about Bastion's capture in order for Fel to secretly gather his forces, and if Draco and Krieg rescued Marasiah, Imperial forces would track Draco and Krieg back to Bastion, exposing Fel. Despite this, Draco and Krieg disobeyed Fel, and went to rescue Marasiah on Vendaxa, where she and Astraal Vao, a Twi'lek from the Imperial Mission, were trapped by Talon. Krieg and Draco were able to save them from the Sith with help from Cade Skywalker, the last remaining heir of the Skywalker family. However, the mission revealed Fel's presence on Bastion.

Sith intrigue
"Be careful Maladi, that you do not scheme for scheming's sake. Do not become so enamored of your plotting that you lose sight of your goal&hellip;the death of Roan Fel."

- Darth Krayt



Having established control of Bastion and the surrounding space, Fel’s agents approached Admiral Stazi with the offer of an alliance against Krayt’s Galactic Empire. The Empire would be represented by Captain Mingo Bovark while the Alliance Remnant would be represented by Stazi himself. Their venue would be the neutral space station known as The Wheel in the Mid Rim. However, the Sith Empire learnt of these secret negotiations and dispatched Calixte, under the guise of her alter-ego Morrigan Corde and Sith assassin Jor Torlin to sabotage the meeting. Their plan involved using advanced technology known as the Command Override Limpet Droid. The C.O.L.D.s would attach themselves to a vehicle's hull, hack into the onboard computer, and order it to open fire.

After attaching to Bovark's Nune-class Imperial shuttle, the C.O.L.D.s caused the vessel to open fire on Stazi's Alliance shuttle. Warned of the attack over his personal comm unit, Stazi assumed the entire conference had been an elaborate Imperial ruse. This led to a brief scuffle between the Alliance and Fel delegates which ended any possibility of an alliance. Intervening to break up the fight, the station administrator Pol Temm expelled the Imperial delegation, forbidding them or any other elements of Fel’s forces from returning. Stazi was allowed to return to his shuttle and depart the station. Meanwhile, Corrde and Torlin resumed their manhunt for Cade Skywalker but turned on each other. In the ensuing skirmish, Torlin was slain.

Having learnt about the whereabouts of Emperor Fel following a confrontation on Vendaxa, Darth Maladi, the Director of Sith Intelligence and Assassination, dispatched Darth Kruhl on a mission to assassinate Fel. Aware that a frontal assault on the fortress world would only stretch the entire Sith fleet thin, the Sith opted for dispatching an assassin to deal with Fel. Due to the high level of security, Maladi’s operation involved inserting Darth Kruhl onto Bastion by using the defection of Governor Vikar Dorn and the entire crew of the Pellaeon-class Star Destroyer Dauntless as a cover. The reappearance of Fel on Bastion had encouraged elements of the Imperial military to defect over to Fel.

While Kruhl succeeded in infiltrating the Pellaeon Gardens where Fel was meditating, he was slain during the subsequent duel by the Emperor. Learning of Dorn’s deception, he ordered the execution of the entire crew of the Dauntless with the exception of Dorn himself who was allowed to return to Coruscant where he was slain by a furious Maladi. Consequently, Fel along with Stazi remained a rallying point for opposition to Darth Krayt’s Galactic Empire.

Mission to Coruscant
"I am a Jedi. I do not fear death. At this moment, in this terrible, once serene place, I think I feel greater happiness, a deeper peace, than you will ever know."

- Trey'lis before his death at the hands of Darth Krayt

Seeking to atone for turning in fellow Jedi Hosk Trey'lis to the Sith authorities, former&mdash;Jedi&mdash;turned&mdash;bounty hunter Cade and the crew of the Mynock infiltrated the Imperial capital of Coruscant. After evading Imperial security forces and criminals alike, Cade infiltrated the Temple of the Sith and attempted to rescue Trey'lis. However, they were ambushed and overpowered by Darth Talon and Darth Nihl.

In captivity, Cade was tortured while Krayt attempted to coerce the former Jedi to join his One Sith. Burning with hatred towards those who had murdered his father, Cade refused to cooperate. In an attempt to draw Skywalker closer to the dark side, Krayt had his companions Jariah Syn and Deliah Blue infected with Yuuzhan Vong Yorik-Kul coral seeds that mutated their bodies using the dark side. Cade had no option but to help both of his friends by using his anger to cure them at the cost of tapping into the dark side. Bowing to pressure, Skywalker agreed to join the dark side on the condition that Syn and Blue were released. Krayt accepted this deal and subsequently invited Cade with Talon and his most loyal Sith adviser, Darth Wyyrlok, to his chambers. There, Krayt surprised Cade by showing him Kol Skywalker's lightsaber encased in transparisteel, giving Cade's father a place of honor. Cade was further surprised when Krayt revealed his knowledge about the Jedi and his true identity of A'Sharad Hett, a Jedi General during the Clone Wars and a survivor of the Great Jedi Purge. Krayt then recited the story of his duel on Tatooine against Obi-Wan Kenobi, near the Lars homestead, and how he was cast out of both Tusken and Jedi society.

After some further confrontation, Cade agreed to submit to a Sith training regime under the tutelage of Talon. However in reality, he was pretending to accept their teachings and to escape at the next opportunity. During a session in the Embrace of Pain, Cade managed to free himself and attempted to escape, but was caught by Talon. He was taken back to Krayt, where he was ordered to kill Hosk Trey'lis or die, but Cade refused to kill the Jedi. Krayt then killed Trey'lis himself, evoking Cade's anger. But Cade then received a vision of his father, telling him "That which can heal, can also break.".

In the subsequent duel, Cade took on Krayt and his Sith acolytes, wounding Darth Nihl. Just as their duel was reaching its climax, Morrigan Corde blasted open the window behind them, shooting Krayt in the back. Cade then jumped out and was rescued by Jariah Syn aboard the Mynock, who pulled him inside. The Mynock then escaped the planet and jumped to hyperspace, but not before Corde revealed herself to Cade over a comlink. Corde revealed herself to be his mother, but when Cade demanded some answers, she replied that he wouldn't be getting any. Unbeknownst to him, Krayt was planning on breaking him, using his power to heal himself and then kill him.

Raid on Dac
"We are in danger of becoming just another pirate fleet, raiding for supplies. We need to make military strikes, and for that we need the Imperious!"

- Admiral Gar Stazi

The planet Dac in the Outer Rim Territories was a key manufacturer and supplier of warships for various galactic powers. Prior to the Yuuzhan Vong War, the planet had been a prominent supporter of the Galactic Federation of Free Alliances, as well as the New Republic and Rebel Alliance that preceded it. Under Imperial occupation, the Quarren had gained control of the planet and the Mon Calamari Shipyards were an important supplier of warships for the Imperial Navy. Despite this, several key Mon Calamari and Quarren leaders were sympathetic to Stazi’s Alliance Remnant and provided spare parts, bacta, recruits as well as intelligence.

Former Alliance Triumvirate member Gial Gahan learnt that the new Advanced Star Destroyer prototype Imperious was undergoing the final stages of construction in the Mon Calamari Shipyards. Capturing the Imperious would allow the Alliance Remnant to switch from hit-and-run raids to engaging in full-scale military offensives. Hatching a plan to capture the prototype warship, the local resistance sabotaged the computer systems that controlled the Shipyards automated defense systems, allowing an Alliance task force to enter the system and hijack the new Star Destroyer.

However, former Triumvir Gahan was unaware that Imperial Admiral Dru Valan had planned a trap for Stazi's forces. Stormtroopers on the Imperious ambushed the Alliance commando units while Valan's Outer Rim Third Fleet appeared at Dac, trapping Stazi between his fleet and the planet's defense systems. Valan contacted Stazi and told him to surrender or die. However, he was unaware that the latter been prepared for his trap all along and had set up one of his own. The Mon Calamari resistance fighter Monia Gahan had seized control of the shipyard guns used them to bombard Valan’s fleet in coordination with a barrage by Stazi’s forces. The combined fire-power of the Alliance fleet and the shipyard's guns inflicted heavy damage on the ships of Outer Rim Third Fleet.

Meanwhile, the stormtroopers that had re-seized the Imperious were actually Alliance troops under the command of Hondo Karr. They hijacked the Advanced Star Destroyer and got it to one of the Alliance bases. Having achieved their objective, the Alliance evacuated the system. During the ensuing escapade, Stazi’s flagship the Indomitable was crippled by enemy fire but he managed to escape. Instead, Captain Yorub took command of the Indomitable and, despite a desperate barrage of fire from Valan's fleet, rammed the ship into the shipyards, destroying a third of them and damaging a quarter.

The battle was a major military and political victory for the Alliance. Not only had they escaped with minimal casualities, but they now possessed a ship that could out-gun the Empire's best ships. In contrast for the Sith Empire, the battle was a source of embarrassment since it undermined Imperial power. In retaliation for their assistance to Stazi, Darth Krayt retaliated by unleashing a genocidal purge against the Mon Calamari, exterminating one-tenth of them and ordering the rest to be placed in work camps. The first to be executed were the members of the Mon Calamari Council though Quarren dissenters were also targeted.

Unbeknownst to both the Alliance and the Sith Empire, Emperor Fel’s agents had sabotaged the Imperious. Three sets of explosives had been rigged to destroyed the ship as soon as its weapons were brought online, which was expected to occur far enough from the shipyards so that the Mon Calamari would not be blamed. As the Alliance was still considered a potential ally by Fel, Imperial Knights Treis Sinde and Sigel Dare rescued Gahan and, at Gahan's insistence, numerous other downed Alliance personnel so that they could reach the Alliance fleet and warn Stazi. Following the operation, Imperial Knight Sigel Dare revealed how to disarm the bombs on the Imperious. Impressed by their actions, Stazi agreed to reopen negotiations with Fel's forces for coalition against the Sith. Master Sinde remained behind to establish contact with the Mon Calamari resistance.

A coup
"My vision&hellip;my dream&hellip;for One Sith&hellip;will live! "It is a magnificent vision, my Lord. Sometimes, for the dream to live&hellip;the dreamer must die."

- Darths Krayt and Wyyrlok, shortly before Wyyrlok killed Krayt



Despite his position as Dark Lord of the Sith and ruler of the Galactic Empire, Krayt's grip on power was also challenged by his affliction. Decades before the Sith–Imperial War, A'Sharad Hett, who would become Darth Krayt, had been captured by the Yuuzhan Vong and implanted with their Yorik-Kul slave seeds. He eventually escaped captivity and founded the One Sith order which adhered to the Rule of One. In contrast to the earlier Rule of Two which limited the Sith to one Sith Lord and one apprentice, Krayt’s Sith order consisted of many Sith subservient to one Dark Lord. Though able to combat the effects of the seeds through his growing strength in the dark side of the Force, Hett was slowly losing his battle with them. By 137 ABY, he had assumed the mantle of Dark Lord and restyled himself as the Dragon of the Sith, but the coral seeds still threatened to turn him into a mindless shell of a man.

For years Krayt was able to sustain himself through healing trances and extended periods of stasis, Krayt consulted the holocrons of earlier Sith Lords but was denied any assistance for disregarding the Rule of Two and therefore being a pretender to the Sith legacy. He was looked after by the most trusted of his servants, the latest of them being Darth Wyyrlok the third. Despite being the most learned of Krayt's Order in Sith lore and ritual, Wyyrlok was unable to find a way to cure that which afflicted his Master. Thus, he consulted a holocron in his possession, one that belonged to an ancient Sith Lord named Darth Andeddu, who was known to have reanimated his flesh after his own death. Wyyrlok then traveled to the Deep Core to Andeddu's homeworld of Prakith, searching for information that would assist Krayt.

Wyyrlok managed to find Andeddu's Keep, where he encountered a previously unknown Sith cult called the Malevolence&mdash;one that worshiped Andeddu and refused to allow Wyyrlok further entry into their domain. In the ensuing skirmish, he killed all the cultists save one named Gerlun, who revived Andeddu's deceased corpse at the cost of his own life. Andeddu then engaged Wyyrlok in a duel of Force abilities, a battle that Andeddu ultimately lost. With the ancient Sith Lord dead for a second time, Wyyrlok returned Andeddu's body to its sarcophagus and sealed it within.

Wyyrlok's mission was partially unsuccessful, as he was still unable to obtain any information in Andeddu's vast collection of Sith lore that would help him in the preservation of Krayt's life. However, he came to the conclusion that Krayt's own doubts that he would not achieve his dream of a stable galaxy under Sith rule fulfilled were a significant contributor to his affliction. An opportunity transpired following an attack on the Imperial garrison on the legendary Deep Core world of Had Abbadon by a mysterious female Jedi, Skywalker and a force of Jedi and Imperial Knights. The female Jedi was the ancient Jedi Knight Celeste Morne who had been kept alive by the Muur Talisman&mdash;an ancient Sith relic created by the Sith Lord Karness Muur which was capable of turning other sentients into mindless Sithspawn known as Rakghouls. While the talisman kept Morne alive beyond the natural human lifespan, she was a captive of Muur until he found a Force-strong individual he could possess. The sole survivor was Darth Reave who succumbed to his wounds and became a Rakghoul but not before telling Krayt of Skywalker’s presence.

Krayt and his advisers then received a transmission from Had Abaddon. Under the guise of the Jedi woman, Karness Muur contacted Krayt and presented him with none other than Cade Skywalker. Muur then issued an invitation to Krayt&mdash;one that he was to answer alone, or both he and Skywalker would die. Krayt accepted the invitation, albeit with three of his Sith Lords accompanying him, and set out for Had Abaddon with intentions of capturing Skywalker once and for all. As they traveled to Had Abbadon, Wyyrlok surmised that Muur would not divulge any secrets, and rather sought to control Krayt through his talisman. However, Krayt was desperate to find a cure for himself as his life was nearing its end.

On the surface, Muur offered an alliance and began to modify Krayt's body. Suddenly, everything was revealed to be a trap, as Cade's allies were waiting in secret. Muur, however, took control of Celeste and planned to take Krayt's body for his own. During the fight, Krayt was stabbed by Azlyn Rae, electrocuted and Force-pushed off of the cliff by Morne/Muur, and seemingly fell to his doom. At the bottom of the cliff, he was discovered by Darth Wyyrlok, who believing his master to dead, ordered his body to be taken back to Korriban.

To his surprise, Krayt woke, having cushioned his fall with the Force. He asked Wyyrlok to take him to a bacta tank in order to regain his strength, but the Chagrian Sith Lord electrocuted his master in response, seemingly killing him. He then placed Krayt's corpse in a stasis chamber within XoXaan's Temple of Korriban, hiding the truth from the other Sith by claiming that his master had merely been wounded in combat and forced into seclusion. Wyyrlok assumed the position of Regent, claiming to rule on behalf of Darth Krayt and continuing his predecessor’s policies including eliminating his opposition and inducting all beings in the galaxy into the ranks of the One Sith.

Against a common foe
"I am Admiral Gar Stazi, last Admiral of the Galactic Alliance! I do not, have not and will never take an order from any Imperial"

- Admiral Stazi



Following the events on Dac and Had Abbadon, a number of allied systems allowed ships from their planetary fleets to join the Remnant. Admiral Stazi led the fleet of Alliance warships in a joint naval operation against the Coruscant Third Fleet at the Imperial stronghold of Ralltiir with forces loyal to deposed emperor Roan Fel. The purpose of the attack was to capture ships to bolster their fleets and to recruit loyalist Imperials, while at the same time strain the Siths' ability to maintain control in the Outer Rim. While the Sith fleet commander Admiral Peto Kelsan agreed to surrender his fleet and to kill those who resisted, one ship refused to do so&mdash;the Steadfast, under the command of Captain Vaclen Tor.

Tor who understood Stazi and Fenel's plans, refused Fenel's orders, causing the Fel loyalist Admiral to ordered all of his Fleet, as well as that of Kelsan, to fire on the Steadfast. Kelsan refused to comply with this new order, rescinding his previous order and ordering his crew to self-destruct and abandon their ships. When Fenel ordered his fleet to open fire on the escape pods, Stazi protested and ordered the Alliance fleet to shield the Sith-loyal escape pods and the Steadfast. By these actions, Stazi reiterated that his forces would not employ the tactics used by Sith-Imperial forces and was an equal to Fel rather than a vassal. While the allied forces succeeded in forcing the Sith fleet to surrender, this victory was tarnished by differences between Stazi and Edouard Fenel, Admiral of the Bastion Second Fleet.

Following the Battle of Ralltiir, Stazi relocated his fleet to the Arkanis sector in the Outer Rim where Alliance forces participated in a mission to evacuate Mon Calamari refugee from Napdu in anticipation of a Sith attack. The local Hutt ruler Azzim Anjiliac Atirue was an ally of the Alliance and was sympathetic to the plight of the Mon Calamari. During this period, Stazi came into contact with surviving members of the New Jedi Order. The Jedi delegates, with the blessing of the surviving Jedi Council members at the Hidden Temple, informed Stazi on their hope to ally with the Alliance against the Sith Empire. In addition, Stazi learned of Cade Skywalker's involvement in the assassination of Darth Krayt.

While in the midst of negotiations with the Jedi, the Alliance fleet was ambushed by the Sith-loyalist First Coruscant Task Force, under the command of Admiral Krion Grail. During the battle, the Mon Calamari Shipman Tealart attempted to assassinate Stazi but was foiled by the Jedi. The Alliance fleet retreated into hyperspace but was unable to shake-off their Imperial pursuers since the latter were tracking the fleet’s comm frequency vibrations. However, Stazi's second-in-command Captain Jhoram Bey sprung a trap by using the flagship Alliance to lure Grail’s forces into the firing range of the re-assembled Alliance fleet. Sustaining considerable damage, the Sith-loyalist fleet was forced to retreat. Victorious in battle, Bey ordered all Galactic Alliance comm frequency vibrations changed before proceeding to the next rendezvous point.

Fortunately for the Alliance, Admiral Stazi recovered from his wounds. In the aftermath, Stazi met with Tealart in the Alliance's brig. Tealart admitted his guilt and explained that Sith agents had contacted him and threatened to kill his entire family on Dac if he refused to cooperate with their plot. With his family threatened, Tealart agreed to cooperate with these agents. While Stazi forgave him and agreed to do his best to rescue his family, Stazi did not pardon Tealart due to the severity of his crime. In accordance with Alliance law, Tealart would be tried and executed for treason.

The final protocol
On Dac, the Sith-inspired Genocide had culminated in the deaths of an estimated ten percent of the Mon Calamari population. In an attempt to cower opposition to the Sith, the genocide was widely broadcast on HoloNet. After Darth Krayt left the planet, Darth Azard, a Quarren Sith, was left to oversee the genocide with the aid of Vul Isen, a Force-sensitive Givin Sith scientist. While thousands of Mon Calamari were sent to extermination camps, where they were left without food or medical aid so they would die of disease and starvation, others fled to the deep oceans of Dac, where they were hunted down by the Imperial Army. The Sith-inspired genocide was resisted by the Mon Calamari Rangers, a resistance organization that waged a guerrilla war against Imperial forces and aided in the escape of refugees. The Rangers were aided by Master Sinde, an Imperial Knight.

During a brief skirmish, Sinde and the Rangers turned the tables on an Imperial Army patrol under Commander Sturves which included seatroopers, Shark fighters and one Acklay Battle Fortress. The poor performance of Sturves' forces during this operation exposed a brain-drain in the Imperial military created by the defection of many able officers and personnel to Emperor Fel’s Empire-in-exile. Due to his expertise on biological warfare, Isen was assigned the task of overseeing the genocide. Since Krayt wanted only the Mon Calamari eliminated and not the Quarren or any of Dac's other native species, Isen would not be able to release experimental viral organisms to wipe out all life on the world. Following some consultation, Isen settled for developing a "Sea Leviathan"&mdash;an aquatic variant of the Leviathan&mdash;alchemically bioengineered Sithspawn created by Dark Jedi during the Hundred-Year Darkness.

The creature, when completed, would be able to eliminate the remaining Mon Calamari on Dac. Though semi-sentient, the Sea Leviathan would absorb the life energies of those it killed, becoming sentient and driving it to think like a Mon Calamari, enabling it to better locate their hiding places. Isen spent weeks developing the creature in the gaping, underwater Soheras Trench, reaching the trench via an Imperial Aquatic Terrain Armored Transport. Following development, the Sea Leviathan was first tested on Mon Calamari inmates at Imperial Extermination Camp 28. Impressed the efficiency with which the Leviathan consumed its prey, the Sith Leviathan was deployed into the open oceans of Dac to hunt down Mon Calamari refugees and to lure the Rangers out of hiding.

Isen and Azard followed the Sea Leviathan in their AT-AT swimmer to Devil's Crevasse on Dac's ocean floor, where the beast interrupted a reconnaissance mission undertaken by two Mon Calamari Rangers in Krakana underwater fighters. However, one of the Rangers, Shonmai escaped back to the Ranger Grotto and alerted her fellow Rangers, who were under the leadership of Sinde. While Isen, Azard, and their Sithspawn prowled around Devil's Crevasse, the Rangers devised a plan of attack that involved sacrificing the refugees to the Leviathan while they attempted to disable the Sith's AT-AT swimmer. They met the Sea Leviathan just as it approached the outskirts of the Crevasse, and a battle quickly ensued. Despite the deaths of many Mon Calamari refugees, the Rangers succeeded in disabling the AT-AT. Further losses were averted by the appearance of the devilsquid&mdash;non-sentient fauna which resided within the Crevasse and had been disturbed by the commotion. Before the devilsquid could join in the fray and besiege the refugees, Master Sinde used the Force to command them to attack Sea Leviathan. Unable to withstand the combined assault of the devilsquid, the Mon Calamari Rangers, and the Imperial Knight, the Sea Leviathan was dragged into the abyss of Devil's Crevasse, never to be seen again.

Only Isen and Azard survived the battle but were undeterred in their resolve to continue the Genocide. Unwilling to squander more Imperial resources on the systematic extermination of the Calamari and bloodied by defeats at Ralltiir and the failed attempted to annihilate the Alliance Core Fleet, Darth Wyyrlok ordered Isen to execute the Final Protocol: the extermination of all life on Dac. This involved contaminating Dac's oceans with viral spores, which would be carried by oceanic currents and kill every life form on the planet within a week. Azard and the pro-Sith Quarren leadership protested, pointing out that the Sith-allied Quarren would also be affected. Wyyrlok was unmoved, though he allowed the Quarren to begin evacuation of Dac without helping or hindering their efforts. Wyyrlok's plan was for using a two-pronged operation to deal a serious blow to his Alliance and Fel foes. If successful, the ambush on Agamar would capture Fel and the poisoning of Dac would lure Admiral Stazi and the GA fleet into a trap.

Within three days, Dac's oceans were covered with the bodies of the dead. This led to the deaths of more than eighty percent of the planet's population. However, total annihilation was averted by the efforts of the Alliance and various individuals to evacuate as many survivors as they could. An Alliance fleet entered the Dac system, driving away the weak Imperial defenses and allowing a civilian evacuation fleet to evacuate many refugees. While the bulk of the evacuees were Mon Calamari, the armada also managed to evacuate large numbers of Quarren, Moappa and Whaladon. The Outer Rim Third Fleet attempted to ambush the Alliance and evacuation fleet but were foiled by kamikaze ships loaded with ion bombs. The arrival of Fel's Star Destroyers under General Jaeger forced the Sith to retreat, allowing the allied forces to evacuate twenty percent of the planet's population.

The hunt for the Butcher of Dac
Word about the Massacre on Dac soon reached Cade. He decided that the "Butcher of Dac" to be the first target of his crusade that would inflict the Sith with a severe blow. Using intelligence from the Sakiyan Naxy Screeger that indicated Isen was located on the planet Daluuj, they raided the Sith scientist’s laboratory, but discovered a group of Imperial stormtroopers instead of Isen they were looking for. While Syn planted timed explosives, Skywalker and Sazen engaged a group of Sith before the last remaining Sith revealed to him the whereabouts of both the scientist and his planet-killing toxins. He also revealed only that Isen had previously used Daluuj as a base and had left no secrets behind. The raiding party left the Sith to die when the base exploded.

Several Mon Calamari survivors fled from their homeworld to Da Soocha in the remote Cyax system. The Hutt Azzim Anjiliac Atirue owned a spa at the Hutt Temple of Maya Armus on Napdu, the fourth moon orbiting Da Soocha. In response, the Sith Empire sent in the First Sith Imperial Strikeforce under Isen and Darth Azard to punish Azzim for sheltering Mon Calamari by bombing Da Soocha’s oceans with deadly toxins. Upon arriving above Da Soocha's orbit, the War Hammer deployed its Sith-Imperial bombers of Squadron Quad Victor that would drop the deadly toxin into the oceans of Da Soocha; exterminating all life on that world. These bombers quickly accomplished their mission and return to the War Hammer.

Azard also ordered the bombardment of Napdu and the secondary deployment of stormtroopers to mop up all possible survivors. Maya Armus was bombarded, killing most of the inhabitants including the Hutt Azzim. Several civilian freighters attempted to escape the Imperial attack but Darth Rauder, aboard her Sith Fury, ordered Skull Squadron to destroy them. On the ground, stormtroopers led by Sergeant Harkas eliminated the remaining survivors. One of his subordinates Corporal Trask showed disapproval of the ethics of his Sith masters' actions; but Harkas reasoned that they were only following orders and killed an injured survivor to support his argument.

On the Hutt capital Nal Hutta, Azzim’s uncle Vedo received a recording of the Sith atrocities on Da Soocha. He subsequently convened a meeting of the Hutt leadership on Nal Hutta to consider entering the war on the side of the Galactic Alliance Remnant and the Empire-in-exile. This was where Cade himself received a transmission from Queen Jool who requested the former’s presence at this meeting. There, they hired his team on a mission to kill Isen.

Isen and Azard established a laboratory on Utapau, where he experimented on native Utai and Pau'an subjects. He planned Gar Stazi's assassination and a new plague which would adapt to any living species.

Skywalker's comrades Jariah and Blue subdued Isen's assassin, however, while Cade and Sazen confronted Isen and Azard. Isen tried to escape while Cade gave chase. On the ledge, Isen ignited his lightsaber and fought Cade. During the duel, both sensed Darth Krayt, who had been resurrected, and soon after, Isen jumped into the sinkhole to release the vial. Cade leaped afterwards, and using the Force to catch up with Isen, sliced Isen in half before retrieving the vial containing the virus intended to eradicate Utapau, saving the planet.

Aftermath
As of 139 ABY, the Temporary Archive for Integration of Materials Related to the Second Imperial Civil War was established on Coruscant.

Behind the scenes
The Imperial Civil War is the primary backdrop for the stories of the Star Wars: Legacy series of comic books, with the exception of Issue 8, which depicts the Sith–Imperial War and explains how it leads to the latter conflict.

When asked whether the events in Broken were the same as the Sith–Imperial War, John Ostrander replied, "Two different wars. In fact, Roan Fel's activities might be likened more to an insurgency so far than an actual war. It's all been hit and run with him so far, as he notes."