- "It is an honor to stand before you, for you represent the freedom and the future of our galaxy. The once-great Republic and Jedi Order have become victims of their own ambitions, and the Supreme Chancellor is no more than a pawn of corporate monopolies. As a people you called out for change, you called out for leadership, and I humbly answered that call. Together we challenged the system. We asked for equality. And how were we met? With war! The Jedi secret army of clones was revealed, and their treachery was far greater than we could have imagined! Countless living beings—these clones the Jedi created—have been sent to their deaths, while we sacrifice mainly droids. Our soldiers of flesh and blood are willing participants! They are your fathers and sons, mothers and daughters, who fight not because they were grown and designed to do so, but because they know in their hearts that they are fighting for a just and noble cause!"
- ―Head of State Dooku addresses a gala of Separatist dignitaries
The Confederacy of Independent Systems (CIS), also known as the Separatist Alliance, the Separatist State, and commonly referred to as the Separatists, was an unrecognized, galactic, democratic, and confederate government that existed during the Clone Wars. In addition to the secret support of several mega corporations, including the Trade Federation and the Commerce Guild, the Confederacy was formed by thousands of secessionist star systems on the grounds of excessive taxation and corruption within the Galactic Senate. The secessionist movement that began in 24 BBY would lead to a political crisis in which tensions escalated between the newly-formed alliance and the reigning Galactic Republic. In 22 BBY, the Separatists and the Republic went to war using their respective military forces—the Separatist Droid Army and the Republic clone army—resulting in a pan-galactic conflict for the first time in a millennium.
The following three years would see the Clone Wars wage across the galaxy with the Separatists rapidly attempting to bring the Republic to its knees. Unknown to the majority of the galaxy, however, the war was merely a ploy—Supreme Chancellor Sheev Palpatine, the leader of the Republic, was a Sith Lord called Darth Sidious, to whom Head of State and Count of Serenno Dooku answered. Towards the end of the conflict, the Confederacy suffered several major defeats in the Outer Rim Sieges as the end of the war approached. After Dooku's death, the Separatist Council was executed on Mustafar. With the subsequent shutdown of the droid army, the state rapidly collapsed as the war came to an end. Following the end of hostilities, trade groups that had supported the cause were nationalized, and most of its remaining star systems rejoined the Republic successor state; the Galactic Empire, whether voluntarily or under threat while some elements fragmented into several holdouts.
For one thousand years, the galaxy had been governed through the Galactic Republic. A democratic union centered on the capital world of Coruscant, the Republic was ruled by the Galactic Senate led by an elected Supreme Chancellor. With the assistance of the Jedi Order acting as peacekeepers, the Republic enjoyed a millennia without large-scale war. However, as time went on, the government of the Republic became weak and corrupt.
During this era of peace, heightening political tensions arose within the Republic a decade before the Clone Wars, such as when a group of usurpers on the planet Halcyon became discontent with the world's membership and wanted their world to be able to manage its own affairs.They kidnapped several members of Halcyon's planetary leadership and held them in a remote fortress where they prepared for assault while attempting negotiation with their hostages. Internal negotiations failed and led the Senate to eventually authorize the Jedi Order to intervene on Halcyon as mediators and enforcers if necessary.
The Invasion of Naboo by the Trade Federation exposed the unwillingness and inability of the Senate to resolve the crisis, which ended only after the Gungans and Royal House of Naboo united and forcibly ended the occupation. This lack of action was a result of years of corrupt and ineffectual governance by the Republic that had became mired in bureaucracy and layers upon layers of increasingly complex legal precedents, treaties, and obligations. The commerce guilds and trading corporations had also become disillusioned after laws were passed that would introduce taxes affecting all significant trade routes, implemented such that they would have the greatest impact on the poorer outlying star systems. These worlds were often forced into accepting one-sided deals and refused military protection, as the Republic continued to prioritize honoring centuries old agreements predating the admission of outlying planets. Gridlock in the senate grew, as the number of votes needed to pass any type of legislation turned it increasingly into a place where senators bartered favors, earmarks, and votes for personal power without regard for their constituencies or the greater good of the Republic. Some began to believe that any attempt at change would require radical thinking and extreme actions, leading to discussions of secession from the Republic.
Secession from the RepublicEdit
- "I am committed to the idea of a galaxy ruled by an enlightened leader, with laws that apply universally—not one set for the Core Worlds, another for the Outer Rim worlds."
"An autocracy, guided by the count of Serenno."
"I am ambitious, but not to that degree."
- ―Count Dooku and Governor Wilhuff Tarkin, during their final dinner together before the onset of the Clone Wars.
The first declaration of secession can be traced back to Count Dooku's denouncement of the Republic after commandeering a HoloNet relay station in the Raxus system, after which some believed he was merely one step ahead of Republic assassins. The fallen Jedi Master's words of inflammatory rhetoric would find receptive audiences among young intellectuals in Mid and Inner Rim universities. Both charismatic and exuding confidence, Dooku's message rallied thousands of individuals by recounting decades of experience within the Republic government and publicizing its hypocrisies, corruption and ineffectiveness. Dooku's rebellious message mesmerized young psyches and spurred them into political activism. As the Separatist Crisis grew more and more heated, Dooku's appearances grew rarer and were announced with much shorter notice, with his message often spurning violence on polarized worlds. Thousands of disgruntled star systems ultimately seceded from the Republic and fully embraced the newly created Confederacy of Independent Systems fiery message of resistance. The idea that the Republic was distant, dispassionate, corrupt, and unworthy of membership ultimately marshalled disgruntled systems into a new galactic government. The agrarian world of Ukio found itself questioning what value it reciprocated for being the breadbasket of the Core Worlds, and after citing a litany of neglect, senatorial representatives of the Abrion sector tendered their articles of secession along with other worlds in the galaxy's hinterlands. The Confederacy also sought to gain prosperous Outer Rim world of Eriadu. With its location at the confluence of the Hydian Way and Rimma Trade Route, Dooku needed Eriadu's allegiance to control the Greater Seswenna and effectively collapse the core back onto itself, undoing millennia of galactic exploration, conquest and colonization. After negotiations and attending dinners with Eriadu's then Governor Wilhuff Tarkin, the attempt to claim Eriadu's loyalty would fail, as Tarkin refused, beveling that an ineffective yet unified galaxy was better than a fractured one.
As the crisis intensified, more systems pledged loyalty to Dooku and the Confederacy across the galaxy. During this period of uncertainty and fears that the Republic would be split into two, the Galactic Senate of the Republic moved towards the passage of the Military Creation Act, which would establish centralized armed forces to protect the thousand-year-old democracy for the first time. Amidala, who was a leading opponent of the proposal was targeted for assassination when she arrived on Coruscant for a vote on the measure. The failed attempt was carried out by the bounty hunters Zam Wesell and Jango Fett, who were secretly hired by the Separatists in an attempt to undermine the Republic. Although the attempt failed, Amidala was forced into protective custody, hastening the eventual passage of the act. 
Shortly after this, the Jedi Order sent Jedi Knight Obi-Wan Kenobi on a mission to the aquatic world of Kamino to investigate the identities of those involved in the plot to assassinate Amidala. After discovering his involvement, Kenobi attempted to arrest Jango Fett. During Fett's escape, Kenobi managed to place a tracking beacon on his ship which allowed him to follow him to the Outer Rim world of Geonosis, where he engaged Fett in a vicious dogfight. Soon after landing on Geonosis, Kenobi discovered that the Separatist Council leading the Confederacy and some key galactic corporate titans had formed an agreement to arm the movement to stand against the Republic secretly and also learns that it was Nute Gunray of the Trade Federation who ordered the assassination of Amidala, as revenge for their defeat at the Battle of Naboo. He was captured shortly thereafter and imprisoned by Dooku, but not before sending a message to the Jedi Council relating what he had discovered. At Amidala's request, Anakin Skywalker attempted to rescue Kenobi, only to be captured himself along with Amidala, with the three of them tied to posts in the Petranaki arena for execution.
Meanwhile tensions between the Republic and Separatist movement peaked after the Republic learned of the size and significance of its army of battle droids, motivating the Senate to grant emergency powers to the Supreme Chancellor of the Republic—a position that was then occupied by Sheev Palpatine, the alter ego of Darth Sidious.
During the attempted execution of Obi-Wan Kenobi, Anakin Skywalker, and Senator Padmé Amidala, a team of two hundred Jedi were sent to the arena to rescue the trio. The Jedi were attacked by a host of battle droids during the attempt and were corralled into the arena. During the battle, Jango Fett was killed while engaged in a duel with Mace Windu after his jetpack malfunctioned. With the battle turning against the Jedi, Dooku gave the remaining Jedi forces a chance to lay down their arms, a choice to which Windu declined. In the next few moments, several Acclamator-class assault ships arrived over the arena, while LAAT/i gunships tore through the droid forces surrounding the Jedi. With the aid of the newly-formed Grand Army of the Republic, the surviving Jedi managed to escape. All the while, the newly formed clone troopers engaged droid forces on the planet's surface, starting the deadly three-year Clone Wars.
- "I have good news for you, my Lord. The war has begun."
"Excellent. Everything is going as planned."
- ―Darth Tyranus and Darth Sidious
War on GeonosisEdit
- "The Jedi have amassed a huge army!"
"'That doesn't seem possible. How could they Jedi come up with an army so quickly? "
"'We must send all available droids into battle!"
"'There are too many."
- ―Nute Gunray and Count Dooku
The arrival of the clones sparked a full-scale battle on Geonosis, with both sides taking heavy losses. Eventually however, the clone army began to gain the upper hand. This forced Poggle to order his soldiers to retreat and hide, but before he joined them, he turned over plans to the Ultimate Weapon — a secret project he had been contracted to build by the Separatists — to Count Dooku. As the battle raged on, Kenobi and Skywalker caught up to Dooku and tried to prevent his escape by engaging in a lightsaber duel, however they were defeated by Dooku with relative ease. Grand Master Yoda came to their rescue and engaged Dooku in a lightsaber battle. After realizing that he was outmatched by Yoda, Dooku fled Geonosis and the Separatist leadership retreated. Though they had suffered a defeat in battle, the goal of the Sith had been fulfilled; the Clone Wars had begun. Shortly the CIS retreat and vacated its first capital world of Geonosis, the Separatists began to seize control of the major hyperspace lanes, separating the Republic from its army.
With the outbreak of hostilities, many worlds either declared openly for the Separatists or declared neutrality, declining to support either side. Some of the neutral worlds banded together into a loose alliance, The Council of Neutral Systems, for mutual negotiation and defense; this was officially merely an advisory group, not a breakaway government. Both sides negotiated with the neutral worlds, with the Republic trying to bring worlds back into the fold willingly if they had not declared for the Separatists due to fears that taking action against ostensibly non-hostile worlds would only increase sympathy for the separatist cause.
The war proceeded on many fronts. A force led by Asajj Ventress and General Whorm Loathsom succeeded in capturing Christophsis, but were soon overwhelmed by the small relief force led by Senator Bail Organa. Later on Teth, the Separatists hatched a plot to deny the Jedi the alliance with the Hutt Clan that they so desperately needed and to establish an alliance with the Hutts themselves. Republic forces attempted to save Rotta, the infant son of crime lord Jabba the Hutt, from the Confederacy, who planned to kill the Huttlet and lay the blame on the Jedi Order. However, Jedi General Anakin Skywalker and his Padawan, Ahsoka Tano, effected a rescue of the Huttlet from Teth and return him to Tatooine, thus gaining the support of the Hutts for the Republic.
After the annihilation of the Republic garrison, Ryloth was occupied and blockaded by the Separatist Droid Army. The army was led by Emir Wat Tambor who oversaw the occupation from the city of Lessu. During the occupation, much of Ryloth was pillaged by the droid army on orders from the Emir. The Confederacy forces were repeatedly attacked by a group of Twi'lek freedom fighters led by Cham Syndulla, but suffered minimal losses. Eventually, the Republic Army assembled a force to liberate the planet, a goal they accomplished after heavy fighting.The Republic captured Emir but his tactical droid escaped with many of the valuables he had looted from the Twi'leks.
The Confederacy meanwhile had developed a superweapon known as the Malevolence. It worked by firing a powerful ion cannon to disable enemy ships before destroying them with a barrage of conventional cannon fire. The ship gained the attention of the Republic after destroying the fleet of Jedi General Plo Koon in the Battle of Abregado. Koon was marooned in an escape pod and rescued by Jedi General Anakin Skywalker. Dooku then ordered the ship to attack an unarmed Republic medical center near the Ryndellia system. Having been alerted to the impending attack, the Republic dispatched a fleet to rescue the medical station. After a fierce battle the ship was finally destroyed when Skywalker tampered with the ship's navicomputer and crashed it into a nearby moon.
Following the loss of the Malevolence, the Confederacy attempted to push on to capture worlds as Malastare, which was of strategic importance to both the Republic and the Separatists forces due to the abundance of natural resources on the planet. The Republic was keen to sign a treaty with the Malastare leadership, however, their plans were put on hold while the Separatist Droid Army invaded the planet. Due to the low number of military forces on the planet, the Republic forces were quickly overwhelmed and, in the face of certain defeat, authorized the use of an experimental Electro-proton bomb. In the ensuing blast, the droid army was shut down and the battle won for the Republic. The leaders of Malastare then proceeded to sign the treaty with the Republic.
Following the discovery of a plan by the InterBanking Clan and the Separatists to build massive new droid foundries on Geonosis, the Galactic Republic launched a second major planetary invasion of Geonosis to shut down the foundries that Archduke Poggle the Lesser had built there. After their discovery on Cato Neimoidia, the Republic dispatched a massive detachment of Clones to retake Geonosis and stop the production of battle droids. Following a difficult landing, the Republic forces managed to establish a landing zone at Point Rain near the factories. The Republic then disabled the factories' ray shield, making way for the rest of the clone troopers to safely land. As Poggle attempted to retake Point Rain, the main droid foundry was targeted by the Jedi, who launched a major offensive against the factory. Unknown to the Separatists, the main assault was actually a distraction that would enable Padawans Ahsoka Tano and Barriss Offee to infiltrate the foundry and destroy the reactor core, thus blowing the factory up from the inside. Following this victory, the Jedi proceeded to destroy the remaining droid foundries on Geonosis, stopping the Separatist plans. Although the droid foundries had been destroyed, Poggle remained at large, having fled off-world.
In order to gain much needed support for their attempt at taking over Mandalore, the Death Watch briefly allied themselves with the Confederacy of Independent Systems. Mandalorian commandos performed sabotage missions for the Separatists against Republic targets. One such mission involved a commando attempting to sabotage a Republic cruiser; the Death Watch commando was captured, but rather than surrender and submit to questioning, he committed suicide. His actions, in addition to false rumors, led many in the republic to believe that Duchess Satine Kryze, the leader of the New Mandalorian government and head of the Council of Neutral Systems, was training a Mandalorian army for the Separatists. The Jedi Council dispatched Jedi Master Obi-Wan Kenobi to Mandalore to meet with Satine and investigate the rumors. At first, the Duchess and her advisers discounted any Mandalorian involvement until Kenobi showed holographic recordings of the Death Watch saboteur. Having no other choice, she reluctantly revealed rumors of the Death Watch's return. The rumors were later proven when a death watch commando bombed the memorial shrine in the New Mandalorian capital of Sundari before committing suicide when Kenobi attempted to apprehend him. Left at the bomb site was a holographic representation of the Death Watch symbol, further highlighting the group's return. During these events the leader of death watch - Pre Vizsla - communicated with Count Dooku who revealed his strategy. He would force the Republic into sending peacekeeping forces to Mandalore. Dooku hoped this would lead the populace to view the Republic as invaders and turn to Death Watch to liberate them.
When Satine journeyed to Coruscant, Death Watch made a second attempt on her life. Mandalore's senator, Tal Merrik, was secretly in league with the Death Watch, and used his senatorial stamp to smuggle several assassin probes aboard the duchess' ship. This attempt failed, and once Satine safely arrived at the galactic capital, the Death Watch reoccupied their base on Concordia as a staging area for their impending invasion of Mandalore. A New Mandalorian scout reported this development to Prime Minster Almec; however, the Prime Minister wasn't concerned because he believed that the Death Watch would never be able to take Mandalore without the support of the public. Meanwhile, the Republic Senate had decided to send peacekeeping forces to Mandalore after being shown forged evidence of a senior Mandalorian minister begging the Republic to send help. With the help of Kenobi, the Duchess was able to uncover the unedited version of the holorecording. After being shown the new evidence, the Republic Senate revoked its order to send peacekeepers to Mandalore. This shut down Death Watch's plans, and they cancelled the planned attack on Mandalore and broke all ties with the Separatists.
Kamino Campaign and Blockade of PantoraEdit
Following the destruction of a Republic monitoring station, the Separatist army, led by General Grievous and Asajj Ventress, invaded the cloning world of Kamino. The aim of the campaign was to destroy the Republic cloning factories and thus deny the Republic more troops, turning the war in the Separatists favor. The droid army was to launch an invasion while Asajj Ventress stole the crucial genetic material needed to produce more clones. However their plan was foiled when Jedi General Anakin Skywalker intercepted Ventress and defeated her following a fierce lightsaber duel. The main droid army was also defeated by the clone troopers. 
During the height of the war, the Trade Federation blockaded the moon Pantora in the Pantora system, in an attempt to force them to join the Separatist Alliance. As part of the conspiracy, the daughters of the Pantoran Chairman Papanoida were kidnapped and held upon the main ship of the Separatist blockade. Following a daring rescue by Ahsoka Tano and Pantoran Senator Riyo Chuchi, the conspiracy was uncovered and the Trade Federation was forced to remove its blockade.
- "Your Republic forces have carried out a barbaric attack on our people! And among the deaths was the very sponsor of the peace accord, Senator Mina Bonteri. With her needless death, I must formally withdraw the proposal for peace offered by our Senate."
- ―Count Dooku
Following a secret meeting between Padmé Amidala and Mina Bonteri, the Separatist Senate approved the start of peace talks between the Separatists and the Republic. However these talks quickly fell apart following a series of plots by Count Dooku to destroy the peace process. Dooku ordered two attacks - the death of Mina Bonteri and a bombing on the Republic capital of Coruscant. Following these, neither side had any desire to continue the peace process. This cancellation came despite heated protests from Amidala who pointed out that the moral responsibility of the war also had to be considered. This led to accusations by some members of the Republic Senate that Amidala had betrayed the Republic.
Loss of VentressEdit
- "Master, I need your help quickly. I am surrounded."
"You have already lost the battle, child. I've ordered your reinforcements to return."
"No! I will destroy the Jedi. I'll show you!"
"You have failed me for the last time. You are no longer my apprentice. And now, you shall die."
- ―Asajj Ventress is betrayed by Count Dooku during the Battle of Sullust
The Separatist fleet began a major space battle against a Republic flotilla, with Asajj Ventress personally leading the Separatists against the Republic. However, the battle would turn when Dooku was ordered to kill his apprentice by Darth Sidious to prove his loyalty. Dooku ordered Ventress' reinforcements to return in an attempt to end his apprentice's life indirectly. Following the destruction of her command ship, Dooku presumed her to be dead and ordered the recall of the armada from Sullust. However, contrary to Dooku's belief, Ventress escaped and survived her ordeal.
Capture of the Temple of EeditEdit
Republic forces were in control of the ancient Temple of Eedit which acted as a front for the Republic's military outpost. In order to gain control of temple, a Separatist Army was sent to attack. The Republic sent two Jedi—Jedi Master Halsey and his Padawan Knox—and several ARF troopers. The Republic troops were able to hold back the Separatist forces and gained the upper hand in the battle. However, in order to test the powers of his new apprentice, Savage Opress, Dooku sent him to Devaron to finish the battle and destroy the Republic forces. Opress mercilessly slaughtered all the clones upon his arrival, including ARF Commander Trauma. Finding the two Jedi in front of temple's door, he attacked Halsey, and although the Roonan fought hard, Opress struck him down. Knox, after witnessing his master's death, attacked his master's killer. However, Opress effortlessly slashed him across the chest, sending him flying into the temple doors, dead. Upon successfully completing his mission, Opress returned to Serenno.
Seeking the Nexus RouteEdit
Following the capture of Jedi Master Even Piell, a highly trained strike force led by Obi-Wan Kenobi and Anakin Skywalker along with his Padawan Ahsoka Tano, attempted to rescue him and his command crew from The Citadel - a high security Separatist prison made specifically for Jedi. The prisoners were of special importance to the Republic because they possessed knowledge of the coordinates for the Nexus Route - a Hyperspace lane which led directly to both the Republic and Separatist capital worlds. During the escape, Piell was killed but the vital information was passed onto Tano. Following a number of challenges, the team managed to escape the prison with the coordinates and most of the former prisoners. 
Fight for FeluciaEdit
- "Form up for counterattack. Lower the gate."
- ―TZ-33, responding to the Republic's offensive
Following the defeat of the Republic during the First Battle of Felucia, the Republic army launched a second invasion attempt. During the invasion the Republic launched a series of major offensives on the planet. In retaliation, General Grievous sent a number of reinforcements to various Separatist outposts on the planet. In response the Jedi intensified their offensive and managed to gain control of the planet and system.
Failure on Mon CalaEdit
- ―Riff Tamson to his Separatist army
Following the assassination of the previous Mon Calamari king, the Quarrens attempted to seize control of Mon Cala with the aid of the Separatists. At the request of Prince Lee-Char, the Republic sent an underwater regiment as reinforcements for the Mon Calamari. After a fierce battle the Quarren and Separatists emerged victorious and enslaved all the Mon Calamari. Not willing to give up on Mon Cala, the Jedi Council sent reinforcements in the form of the Gungan Grand Army from Naboo. During the ensuing battle the Quarren came to the realization that the Separatists were only interested in capturing Mon Cala for themselves. With this in mind they turned on the Separatist forces and defeated them. 
Attempted conquest of NabooEdit
- "Why bring the war to Naboo?"
"How quickly you forget! After all, the war started here years ago."
"You were a part of that first battle?"
"The Sith control everything—you just don't know it!"
- ―Anakin Skywalker and Count Dooku
Dooku conspired with General Grievous and Rish Loo to launch another invasion of Naboo, a plot that would involve turning the Gungans against the Naboo. Minister Rish Loo began influencing Boss Lyonie through the use of a necklace. He influenced Lyonie to order an attack on Theed with the help of the Separatist alliance. After Anakin Skywalker and Jar Jar Binks removed the necklace, Rish Loo attempted to kill Lyonie. Believing him dead, Rish Loo went to the assembled Gungan Grand Army and told them that Lyonie was dead, ordering them to attack Theed immediately. Jar-Jar however, arrived at the event, posing as Lyonie. He denounced Rish Loo and cancelled the order to invade Theed. Rish Loo then fled to his laboratory. Anakin followed Rish Loo, fighting the probe droids sent to stop him. Meanwhile, Grievous and his army landed on Naboo and contacted Jar-Jar (who they believed to be Lyonie) to ask why the attack on Theed had been cancelled. Jar-Jar entered Grievous's lander and attempted to stall the General. Eventually, Grievous figured out that Jar-Jar was not Lyonie, and chased the gungan outside, where he found his entire army deactivated. The Gungan army surrounded Grievous and told him to surrender. Grievous replied by drawing two lightsaber and killing several Gungan warriors. His rampage was stopped however when General Roos Tarpals stabbed him with an electric spear, the cyborg stabbed Tarpals through the heart and killed him. Just before he died Tarpals drove his spear all the way through Grievous allowing the rest of the Gungan warriors to disable Grievous with boombas.
At the same time, Skywalker found Dooku's lair, after following Rish Loo to an ancient cliff-side structure. Unknown to Skywalker, the lair was actually a trap set by Count Dooku, designed to capture Skywalker. Following a lightsaber battle, involving Dooku and several Magna Guards, Skywalker was captured and held hostage by Dooku. Shortly after Skywalker's capture, Padmé Amidala received a message from Dooku on her holoprojector. During the exchange, Dooku told Amidala that he had captured Skywalker. He then demanded that Amidala give back General Grievous in return for Skywalker. She reluctantly agreed and the prisoner exchange took place shortly thereafter. Following the prisoner exchange, the Separatist forces retreated.
Deals with Zygerrian Slave EmpireEdit
The Confederacy had formed an alliance with Queen Miraj Scintel who led the Zygerrian Slave Empire. As part of the deal, the Confederacy attacked a Togruta colony on Kiros and enslaved all of its inhabitants.
However their plans were foiled when the Jedi managed to track the missing colonists to the Zygerrian homeworld of Zygerria. The Jedi Council then sent Anakin Skywalker, Obi-Wan Kenobi and Ahsoka Tano to infiltrate the slave markets where the colonists were being held. During their attempted rescue, Kenobi and Skywalker were captured. Kenobi was sent to a slave processing facility while Skywalker became the personal slave of the Queen. While being held as the personal slave of the Queen, Scientel developed feelings for Anakin. When she was ordered to kill him by Count Dooku she refused. As a punishment for her defiance Dooku killed her. Seeing his opportunity, Skywalker freed Tano and carried the Queen onto a slave ship upon which he escaped.
Following Skywalker's escape, the Queen revealed to him the location of the processing facility where Kenobi and the missing Togruta colonists were being held. Having discovered the location and told the Jedi Council, Skywalker and Tano arrived at the facility. They attempted to break into the facility but failed. Soon after their arrival Republic reinforcements arrived and the facilities defenses were soon disabled. With no hope of escape, the facilities manager Agruss attempted to kill the colonists by dropping them into a volcanic pit. However, his plan was foiled when Tano devised a plan to rescue the colonists. With the successful rescue of Kenobi and the colonists, the Jedi departed the facility and destroyed it. 
- "The Republic recognizes the tragedy of war, but there is nothing we can change that has already occurred."
"Say it aloud before this gathering—as representative for Chancellor Palpatine that you declare, without reservation, the Separatist state legitimate."
- ―Senators Padmé Amidala and Voe Atell
At the height of the Clone Wars, the Confederacy of Independent Systems held a peace conference with the Galactic Republic on the neutral planet Mandalore between representatives of both governments in an effort to end the pan-galactic conflict. The conference was presided over by Duchess Satine Kryze within her royal palace in the New Mandalorian capital Sundari. At the beginning of the meeting, Naboo Senator Padmé Amidala opened up the discussions, leading the Republic senators in the peace negotiations, but she was quickly rebuffed by Senator Voe Atell, who called for the Republic to declare the Separatist State legitimate. However, before the delegates could further discuss their terms of peace, Lux Bonteri, son of the late Onderonian senator Mina Bonteri, interrupted the summit and announced to the politicians that it was Count Dooku that had his mother murdered. This led young Bonteri to soon afterward be escorted out by Separatist security droids, allowing the discussion to continue. Shortly after his escape, however, the negotiations fell apart completely along with hopes of gaining the full legitimacy it sought, however the Confederacy had received some legitimacy as a state by the very notion of the conference having took place.
Having instigated Onderon's secession from the Galactic Republic at the beginning of the Clone Wars, King Sanjay Rash found his regime, which was being backed by the Confederacy of Independent Systems, challenged by a group of rebels organized by the young insurgent Saw Gerrera. The rebels hoped to restore the deposed King Ramsis Dendup to the throne. Seeing an opportunity to engage the Confederacy on another front, the Republic began to fund the rebels with credits and arms to combat Rash's occupational forces from the Separatist Droid Army. The Jedi High Council sent a team of advisors to train the rebels along with some of the 501st Legion who were covertly inserted into Onderon and oversaw training sessions at the insurgency's jungle camp. Midway through the training, the camp was attacked and the lessons escalated into actual combat when a battle droid squadron attempted to exterminate the rebels, however, the newly trained rebels eliminated the enemy droid squad. The rebels then infiltrated the Separatist-occupied capital Iziz, conducting strikes on droid patrols throughout the city. They also targeted Iziz's main power generator to extinguish the battle droids recharging source and also proving they were capable of challenging the Separatists and. Count Dooku sent King Rash reinforcements under the command of the super tactical droid General Kalani.
After the rebels attempted and failed to free the deposed King Dendup, King Rash ordered his public execution. However his plans were foiled when General Tandin and his royal guards sided with the rebels during Rash's attempted execution of Dendup, helping Gorera and her insurgents rescue Dendup, He also pledged the Royal Onderon Militia to their forces. With Steela appointed by Dendup as their commanding general, the joint rebel and royal soldiers pulled out from Iziz, hoping to preserve civilian lives by isolating armed conflict to the eastern highlands. As full-scale fighting began, the rebels used the mountain terrain against the Separatists and despite heavy casualties, won the battle with the help of illegal rocket launchers supplied to them though underworld contacts. Faced with this catastrophic defeat, Dooku contacted Rash and Kalani. Rash explained what had happened and that they would need even more help to defeat the rebels. Dooku refused, not wanting another war to deal with. He commanded Kalani to call back all of the droid forces from the planet. As Rash angrily protested, Kalani shot the deluded king, killing him.
The Carida Incident was the result of a mission undertaken by the Confederacy of Independent Systems who sabotaged the Venator-class Star Destroyer Renown by loading it with rhydonium canisters with the intention of ramming it into the Valor space station, the site of a Republic strategy conference. While escaping Abafar, the D-Squad took refuge in the Venator-class Star Destroyer, on which they planned to return the stolen Separatist encryption module, but they discovered it was overrun by droids. They undertook efforts to disrupt the Confederate plot and stop the ship from destroying a Republic strategy conference in the Carida system.
The Battle of Ringo Vinda took place outside a Separatist controlled space station that surrounded the planet of Ringo Vinda. Initially the battle was turning in the favor of the Republic. However, the battle turned in the Separatists favor when a clone trooper, CT-5385 Tup, malfunctioned and executed order 66 early, killing Jedi General Tiplar. With their momentum lost, the Republic had no option other than to retreat. The unusual behavior of the Republic was noticed by Admiral Trench who reported it to Dooku, who then reported it to Darth Sidious.
The world of Anaxes was attacked by a Confederate fleet under the command of Admiral Trench who besieged the Republic shipyards at Anaxes for weeks on end, exploiting the Techno Union's access to a secret Republic strategy algorithm. Even as the tide of battle began to turn against him, Trench remained intent on annihilating the Jedi and their clone infantry. In a last ditch effort, he activated a bomb beneath the assembly complex on Anaxes. However, Anakin Skywalker infiltrated Trench's flagship and forced the admiral to divulge the sequence to disarm the device. When Trench tried to retaliate, Skywalker drove his lightsaber through his chest killing him and ending the battle.
The Confederacy would attempt to commit a mass genocide on the people of Mahran under orders from Count Dooku. The planet was of strategic importance to the Confederacy because of its vast quantities of natural resources. In response the people of Mahran begged the Jedi Council to send aid. The Jedi responded by sending Jedi General Chubor with a task force of clone troopers. However, they were too late to prevent Separatist forces from laying waste much of the planet, including the capital city. The Republic attempted to escort the remaining Mahranee off world but were stopped when the Separatists launched a massive attack, slaughtering all the civilians, Jedi and clones. After this massacre, Dooku attempted to lay the blame for the tragedy on the Jedi Council. This led the council to finally authorize an assassination attempt on the Count in a desperate bid to limit the war's casualties. 
Attempts on DookuEdit
Towards the end of the Clone Wars, the Jedi Council decided to assassinate Count Dooku to hasten the end of the war. They sent Quinlan Vos under the guise of a bounty hunter to recruit Asajj Ventress, who previously came close to killing Dooku and knew much about him, to aid him in the assassination. Their first attempt on Dooku ended in failure with Vos being captured, with a final plan to assassinate him during the second battle of Christophsis ending in the death of his former apprentice Asajj Ventress.
Destroying Maul's Shadow CollectiveEdit
- "Maul! Your end is at hand!"
- ―General Grievous, as the attack began
As the Separatists pressed on against the Republic, Darth Sidious had brought Maul to the Spire, a prison fortress controlled by the Confederacy of Independent Systems on Stygeon Prime. It was there that Sidious briefly interrogated Maul, and told Count Dooku to find out information about who and where the Shadow Collective leaders were. The goal was to make Maul believe that the Sith wanted to destroy the Shadow Collective, so he would seek out Mother Talzin. Meanwhile, Sidious was followed to Stygeon Prime by two Death Watch warriors, Rook Kast and Gar Saxon, under orders from Mandalore's Prime Minister, Almec to free Maul from the Spire.
After being freed, Maul was tracked to Zanbar by General Grievous along with a Separatist fleet. Dooku ordered Grievous not to kill Maul, simply to defeat and break his forces enough that Maul would seek out Mother Talzin's help. Grievous launched his forces towards the surface, and Maul's troops immediately began firing anti-aircraft weaponry at them. The heavy fire was not enough to repel the ships, however, so the Separatists pressed their attack and deployed all of their forces.
After the Shadow Collective lost on Zanbar, Maul attacked Dooku and Grievous over Ord Mantell which led to Maul make his way into orbit and boarded Grievous' command ship. Grievous disabled the battle droid army after Maul gave him the choice to do so or die, and the cyborg general was taken into custody. Dooku, meanwhile, had engaged and defeated the Nightbrothers in battle, before being captured by the Shadow Collective forces.
Sidious and Grievous arrived to confront Maul and Talzin on Dathomir after finding out where Dooku was being held, the latter of whom had used her magick to take control of Dooku's body. This led to a lightsaber duel, in which Sidious quickly gained the upper hand against the Talzin-controlled Dooku. Talzin appeared in the flesh, returned to her physical form, and held off a Force lightning assault from Sidious and, eventually, Dooku. Talzin sacrificed her own life to allow Maul to escape, as Grievous fatally stabbed the Dathomirian witch through the chest while Maul fled from Dathomir. The Separatists, meanwhile, also attacked Maul's Black Sun and Pyke Syndicate allies, leading the mercenaries to end their alliance with Maul; destroying the Shadow Collective.
End of the Clone WarsEdit
In the war's final days, the Separatist Navy led by Head of State Count Dooku launched an daring attack on the capital of the Galactic Republic - Coruscant. During the battle, Supreme Chancellor Sheev Palpatine was captured by General Grievous and kept on board his command ship. The Republic sent Jedi Generals Obi-Wan Kenobi and Anakin Skywalker to rescue the Chancellor. During their rescue attempt, they were confronted by Count Dooku and engaged him in a lightsaber duel. Dooku initially gained the upper hand, knocking Kenobi out, however, after taunting Skywalker into using his rage to focus his attack, Dooku defeated Kenobi, who was incapacitated and knocked unconscious when the Count used the Force to pin Kenobi to the ground with a metal balcony. However, he was soon overpowered by Skywalker, who cut off his hands and then took Dooku's own lightsaber and held it to his throat along with his own, in a scissor-like way. At Skywalker's mercy, Dooku was sentenced to death by Chancellor Palpatine. Despite the fact that the Count was an unarmed prisoner and that it was against the Jedi Code, he was nevertheless beheaded by Skywalker. After rescuing the Chancellor, they escaped to the bridge where Grievous lay in wait for them. They engaged him in a duel and managed to defeat him, however he managed to escape. Grievous then ordered the fleet to withdraw and became the leader of the Separatist Alliance who fled to Utapau, an occupied world where he hid and met with the Separatist Council where after a brief disagreement with Nute Gunray, ordered both him and the Council to go to the Mustafar system where they would be safe. During his time there, his location was discovered by Clone Intelligence. This led the Jedi Council to send Jedi Master Obi-Wan Kenobi to investigate. Having arrived in secret, Kenobi confirmed the presence of Grievous and ordered a full scale assault on the settlement. During the ensuing battle, Grievous would be killed by Kenobi while trying to flee the sinkhole planet.
During this period, the Republic was laying siege to the Confederacy in the Outer Rim Territories with battles taking place on Cato Neimoidia, Mygeeto, Saleucami, Felucia, as well as Kaller in what was to become some of the most deadly fighting in the whole conflict while on Lokori where for the last four months of the war, elements of the Separatist navy attempted to break through the lunar picket lines of the Bright Nebula Fleet and attack the planet, only sporadically managing to launch attacks against the planet itself. While the CIS planned to capture a system of high importance that would turn the tide of the war in their favor and mounted an attack on the Mid Rim world of Kashyyyk. Due to its status as an important navigational point, the Republic could not afford to lose it. Fighting carried on, on Utapau and Kaller, where the Republic was winning over the Confederacy. The conflict took an unexpected turn as a purge of the Jedi began, and while having no involvement in Order 66 that was authorized by Chancellor Sheev Palpatine (secretly Darth Sidious), it's droid armies on planets such as Mygeeto and Felucia bore witness to the Republic armed forces turning on the Jedi Order who were leading them.
Fall of the ConfederacyEdit
- "The war is over! Lord Sidious promised us peace. We only want—"
- ―Nute Gunray's last words, before being killed by Darth Vader
With the loss of General Grievous, the Separatist Council became the heads of the CIS as the fighting in the Clone Wars ended. Darth Sidious spoke to the Council members via hologram, with Gunray remarking confidently that the plan of the Council had gone just as Sidious had promised. Though Gunray and the others did not know what was about to happen, the Dark Lord promised that his new apprentice would soon arrive to take care of them but he would be sent instead to eliminate the leaders who had gathered on Mustafar. Once Darth Vader landed, he began the final act of the Sith grand plan as he entered the mining facility and slaughtered the Separatists, taking them out one by one with his lightsaber; he also destroyed the B1 battle droids, an OOM command battle droid, and Neimoidian guards and aides who had assembled in the room with their leaders. In rapid succession, Vader executed the Councillors including Po Nudo of the planet Ando, Passel Argente of the Corporate Alliance, and Presidente Shu Mai of the Commerce Guild. He then set his sights on Tikkes of Mon Cala and Archduke Poggle the Lesser of Geonosis. Emir Wat Tambor of the Techno Union, who fled into a conference room, and Rune Haako of the Trade Federation were also soon killed and only Nute Gunray remained who begged for mercy but also was murdered by Vader. After the slaughter, Vader received the order to end the Clone Wars from Emperor Sheev Palpatine by sending a shutdown signal to all Trade Federation Droid Control Ships that would shut down the battle droids of the Separatist Droid Army. This signal would spread throughout the galaxy, such as on Lokori, where last of the Separatists forces were still fighting after having broken through and managed to land on the surface, and had reached the point of breaking the Imperial lines until the Droid Army was shut down. The super tactical droid General Kalani, however, accurately deduced that the shut-down order was a Republic trick, and overridden the command signal for the battle droids under his command and therefore survived the end of the Clone Wars, unaware that it had ended. They were left marooned at their base on Agamar, where they waited for retrieval during the next seventeen years. Kalani's remaining garrison consisted mostly of B1 battle droids and a few droidekas, though they lacked any heavy vehicles or starships capable of leaving the planet but the munitions depot they were protecting at the base kept Kalani and his droids well-provisioned enough to still remain reasonably functional for almost two decades without resupply, but nevertheless this officially ended the fighting with the newly created Galactic Empire and the destruction of the Confederacy of Independent Systems.
Aftermath of the Clone WarsEdit
- "Galen, you're not going to hear this on the nightly holonews, but while the war is essentially won, it's not over. Not here. Not in many systems of the Western Reaches."
"I've heard reports of Separatist holdouts—"
"They're much more than holdouts. Call them what they are: anarchists."
- ―Orson Callan Krennic and Galen Walton Erso
Following the end of the war on Mustafar, most remaining aligned systems to the CIS after its defeat were forcibly occupied by the Republic's successor state, the fledgling Galactic Empire whose Navy began to root out the remaining surviving governing and military holdouts who had not surrendered and stopped fighting for at least four years after the Clone Wars, while criminal organizations composed of re-purposed battle droids such as the Droid Gotra operated in Imperial Center's underground while some escaped notice all together. Seeking to make examples of worlds who continued to harbor secessionist tendencies, worlds like Kooriva, Murkhana and on Raxus, the formal capital of the Confederacy, which still hosted ex-Separatists, became targets of the Empire. One such example, assigned to Moff Wilhuff Tarkin, was on the once loyal Separatist moon, Antar 4. During the genocidal atrocities committed on the moon's population, Imperial forces made no attempt to sort the Separatists from the Imperial loyalists. This served to compel Raxus and other worlds to surrender all former Separatists to Imperial custody, or else suffer a similar demise to that of Antar 4.
Meanwhile in 18 BBY in the Western Reaches, where most of what was left of the Confederacy of Independent Systems had fled with the support of the various planetary populations of former Confederate worlds who were dissatisfied with the lack of reconstructive action in the aftermath of the Clone Wars, then joined the holdouts and thus swelling their numbers in their campaign against the Empire that lasted till 15 BBY. Imperial shipyards like the one in orbit over Kartoosh, just outside of the Western Reaches, served as a repair hub for starships damaged in engagements with Separatists as well as salvage yards for captured vessels. The Bilbringi shipyards also served as a dismantling point for old Separatist warships. The Imperial forces were led by Tarkin, fresh from "pacifying Antar 4," who had been assigned to oversee operations by Emperor Sheev Palpatine himself. Both Tarkin and Lieutenant Commander Orson Krennic would utilize the conflict against the holdouts as a pretext to justify for the appropriation of numerous legacy worlds—worlds legally protected as ecological reserves—advancing the top-secret Imperial construction project occurring above Geonosis.
- "Understand as a Separatist, I fought for freedom but put my trust in a corrupt leadership."
"You were the leadership—a General."
"The Jedi were Generals. Do you truly believe they comprehended the cause they started? Holster your weapon, boy. We are no longer enemies. Perhaps we never were."
- ―Former Separatist General Kleeve to Jedi survivor Caleb Dume
During the Age of the Empire, the tale of the Clone Wars was frequently used as a warning to the Galaxy of what could happen should the Empire and order fail. Separatist military equipment (including battle droids) that survived the war was used by a number of pirate and resistance organizations. A large amount of heavily modified Separatist equipment was used by the Alliance to Restore the Republic; examples include the IG-227 Hailfire-class droid tank and the Armored Assault Tank.
Soon after the Empire's formation, Emperor Palpatine and Darth Vader observed the construction of the Death Star, a super-weapon which had begun construction shortly after the Second Battle of Geonosis by the Republic. With the Separatists defeated and their leaders killed, the Death Star project was taken over by the Galactic Empire, who planned to use it to control the galaxy.
Nineteen years later, the Death Star was used to destroy the planet Alderaan, killing all the inhabitants. The Death Star was later destroyed during the Battle of Yavin when a young Rebel pilot, Luke Skywalker, exploited a serious design flaw to destroy the battle station. This event is often credited with beginning the Galactic Civil War.
After the Alliance to Restore the Republic was re-organized into the New Republic after it won the war, it was decided that the capital of the New Republic would be rotated periodically - addressing one of the main concerns of the Confederate systems.
Leaders of the ConfederacyEdit
The Confederacy had a single Head of State. The position was held, for most of the Confederacy's existence, by Count Dooku, who was secretly the Sith Lord Darth Tyranus and the apprentice of the Dark Lord of the Sith Darth Sidious. After Dooku's death during the Battle of Coruscant, General Grievous assumed command of the Confederacy as a military leader briefly until his own death at the Battle of Utapau. After the loss of Grievous, Viceroy Nute Gunray and the Separatist Council took power. However, like Grievous, their tenant was short lived as they themselves would be killed by Darth Vader during his mission to Mustafar. Aiding them were members of the Separatist Council, made up of various galactic corporations who had pledged full support to the Separatist cause but still deny having links to it while maintaining it connections to the Galactic Republic and wielded considerable powers over officers over the political and military landscape.
The Confederacy of Independent Systems would see several leaders across its lifespan, including:
- Count Dooku, Separatist Crisis — Battle of Coruscant.
- General Grievous, Battle of Coruscant — Battle of Utapau.
- Separatist Council, post-Battle of Utapau - Mission to Mustafar
Operating below the Head of State and Separatist Council was the Separatist Senate, a body of senators that dealt with diplomatic and civilian issues. It was made up of worlds and systems who joined the Separatist cause, including ones that had once been members of the Galactic Republic. The senate was seated on the Confederate capital planet of Raxus. Many loyalists and senators of the Republic believed that the Separatist senators were no more than pawns to Dooku.
- "Our friends from the Trade Federation have pledged their support. And when their battle droids are combined with yours, we shall have an army greater than any in the galaxy. The Jedi will be overwhelmed. The Republic will agree to any demands we make."
- ―Count Dooku to the Separatist leadership
The various commercial entities who joined under the banner of the Confederacy pledged their forces to the Separatist Army and Navy, creating one sprawling group of droids as well as organic forces, and local warriors, and was often referred to as the Droid Army. These ranged from the Trade Federation's battle droids to the security forces maintained by the Commerce Guild, InterGalactic Banking Clan and Corporate Alliance, which donated not only its new B2 super battle droids, but numerous foundries capable of producing thousands more droids for deployment as well as the OG-9 homing spider droids were a common sight on many front lines, and tank droids, droid subfighters, and AATs provided heavy firepower.
The Confederacy of Independent Systems maintained a number of foreign relations with several independent or client states in the galaxy during its political existence. It maintained relations with both independent entities and established a number of puppet governments across the galaxy.
Society and cultureEdit
Count Dooku was the main leader of the Confederacy of Independent Systems who served as a unifying force in the Separatist movement. Many Separatists viewed him as a single, seemingly invincible figurehead to rally around. Some observers like the Jedi Master Mace Windu believed that eliminating Dooku would lead to the disintegration of the Separatist movement. While the Separatist movement had other leaders like Separatist Congress Leader Bec Lawise, Senator Mina Bonteri, General Grievous, the Viceroy Nute Gunray, and Riff Tamson, all the other players within the Confederacy were controlled by Dooku. To boost morale, Dooku traveled to several worlds including Raxus where he gave rousing speeches defending the Confederacy's cause and war effort. Wherever he traveled, Dooku was greeted by large crowds. Despite atrocities like the Attack on Mahranee, Dooku was still respected enough within the Confederacy to be conferred with awards like the Raxian Humanitarian Award.
According to Count Dooku's propaganda, the Galactic Republic and the Jedi Order were the victims of their own ambitions. He also alleged that the Supreme Chancellor was the pawn of corporate monopolies and that the Jedi had secretly created the Grand Army of the Republic to suppress the Confederacy's demands for reforms and equality. While the Republic's clone troopers were regarded as unwilling slaves who were regularly sent to their deaths, the Separatists sacrificed mainly droids. Dooku also claimed that the Confederacy's flesh and blood soldiers were willing participants who were fighting for freedom.
The population in the Confederacy held a mostly non-human majority which was reflected in both its military and political arena as well the galactic corporations who gave support to it, such as the Trade Federation, Techno Union, InterGalactic Banking Clan, Commerce Guild and Corporate Alliance.
During the Battle of Mon Cala, the Separatists exploited tensions between the Mon Calamari and Quarren by backing the latter. Count Dooku also ordered the enslavement of Mon Calamari prisoners and civilians. Despite supporting the Quarren, Dooku made a secret agreement with the Karkarodon leader Riff Tamson to crown him the new King of Mon Cala. The Confederacy later committed genocide against the Mahran species and attacked their homeworld, killing many civilians and refugees. In addition, the Confederacy also issued an order that all Mahrans were to be regarded as extremely hostile and killed on sight.
The Separatist State gained a vast transportation network as systems and sectors broke away from the Republic during the Separatist Crisis which served as means of both civilian and military transport to support it objectives. This included several major hyperspace lanes—which were considered trans-galactic highways—with their knowledge and existence dating back to well before the Galactic Republic. Their control was vital for maintaining an effective means of defense and security during the Clone Wars.
Communication and mediaEdit
Lacking its own official holofeeds network, the Confederacy used unauthorized Shadowfeeds instead that were used by Count Dooku in an effort to spread propaganda during the Clone Wars. Shadowfeeds were created through sabotage of legitimate HoloNet networks. However, Republic Intelligence was able to shut down many of these Shadowfeeds quickly, which eventually led to the creation of the Commission for the Protection of the Republic. The governor of the planet Eriadu, Wilhuff Tarkin, was responsible for frustrating Dooku by providing counter intelligence to shut down his Shadowfeeds during the Clone Wars.
- "As I explained to you earlier, I am quite convinced that ten thousand more systems will rally to our cause."
- ―Dooku, to the Separatist Council
The territory of the Confederacy of Independent Systems varied in size a great deal during the course of its short history. At the beginning of the Clone Wars, the Confederacy numbered at least ten thousand star systems, as well as the various commercial groups, allied under its banner.
Behind the scenesEdit
The Confederacy of Independent Systems first appeared in Star Wars: Episode II Attack of the Clones. Early in production of Attack of the Clones, the various commerce guilds were to all employ the same type of battle droids that were used by the Trade Federation, albiet with different color schemes to differentiate alligence, but it was later decided that having each guild have their own wholly unqiue droids would provide visual diversity.