The Confederacy of Independent Systems (or the CIS), commonly known as the Separatist Alliance or just the Separatists, was a rival government of thousands of worlds which attempted to secede from the Galactic Republic, leading to the galaxy-wide three year long conflict known as the Clone Wars. During the war the Separatists fielded a massive army of battle droids, supplemented by local forces.
The Separatist Alliance was ostensibly led by Count Dooku, but in secret was truly led by Dooku's master Darth Sidious - Chancellor Palpatine, leader of the Galactic Republic, who was playing both sides against each other, in order to manipulate the Republic Senate into granting him dictatorial emergency powers. At the conclusion of the war Count Dooku was killed, the Confederacy was defeated and ceased to exist, and Palpatine transformed the Republic into the Galactic Empire, declaring himself Emperor.
The Decline of the Galactic Republic
The Galactic Republic had ruled most of the galaxy for over a thousand generations, devoted to peace, diplomacy, law and order. Over time, however, the Republic eventually grew stagnant, partially because corrupt politicians in the Galactic Senate and other bureaucrats were more concerned with amassing power and wealth for themselves than with the well-being of the worlds and sectors they ruled over. The Senate's powers became nearly crippled by this corruption, with government gridlock by self-interested factions stalling any meaningful reforms.
Widespread political graft and simply ineffectual leadership led to a gradual decline in the galactic economy as well. In turn, this eventually led the Republic Senate to desperately try to raise funds by increasing taxes on trade routes. This angered many worlds, and most importantly, the massive commerce guilds and mega-corporations of the galaxy. The Republic had ruled in peace for so long that it actually did not possess a standing army, as there hadn't been a full scale galactic war since the formation of the Republic. The commerce guilds, in contrast, maintained their own private security firms, and had the industrial resources to quickly expand them into entire armies of rapidly produced battle droids. In protest of the Republic Senate's attempts to raise taxes, the commerce guilds started getting into increasingly acrimonious trade disputes, and outright military blockades of planets which could not repay their exorbitant debts (such as Naboo).
The Republic's attempt to rein in the commerce guilds through higher taxes utterly backfired: instead, it revealed just how toothless it had actually become, no longer possessing the military, governmental, or judiciary means to control the commerce guilds. Many hundreds of worlds began to openly express that the Republic was no longer serving their interests: at best, too corrupt or ineffectual to protect their interests, and at worst, actively exploiting them. Meanwhile, the commerce guilds were increasingly acting like functionally independent powers, even employing their own armies in military actions.
Some reformers in the Senate, as well as the Jedi Order, tried to salvage the growing crisis as best they could. Indeed, it is possible that if all efforts had been directed towards peaceful reform of the Republic government, they might have succeeded, and conflict could have been avoided. Unfortunately, unscrupulous individuals sought to profit from the Republic's collapse.
Origins of the Separatist Crisis
Some three years before the Clone Wars openly began, various factions that had completely given up on the Republic began formally coalescing into the "Separatist" movement.
Many of these were unscrupulous individuals and groups who sought purely to profit from the breakup of the Republic - particularly the commerce guilds, who wanted to create a new state in which they could run their enterprises free of any government restrictions or taxes. Some were individual worlds that saw secession as an excuse to grab more territory, or act out long-standing grudges against neighboring rival planets. A great many worlds, however, had legitimately become disenchanted with the Republic and particularly, the repeated faliure of every attempt at reforming it from within - such worlds and individuals genuinely came to believe that the Republic was too corrupt to save and represented only tyranny and/or ineffectual leadership. Before long, many prominent Republic Senators started expressing Separatist sympathies.
Chief among those rallying and inflaming the growing Separatist movement was Count Dooku, a former Jedi who had left the order. It was he who brought together the commerce guilds into a single alliance, along with pro-Separatist senators and secession movements from various worlds, and ultimately, organized them into a rival state to attempt to secede from the Republic. This new state was formally termed the "Confederacy of Independent Systems" but was most commonly referred to even by its own members as just "the Separatist Alliance" or simply "the Separatists".
The Confederacy was formalized by a treaty that Dooku brought representatives of the Separatist Council together to sign on Geonosis. While the Republic's Senate desperately still attempted to settle the crisis through peaceful negotiations, the Separatists were already secretly preparing for war, greatly expanding production of battle droids to produce the most massive army in the entire galaxy. The Separatists hoped that an unprovoked first strike would lead to the quick defeat of the Republic and ensure their independence.
In secret, however, the Separatists themselves were merely pawns of the Sith, and never intended to succeed. Count Dooku was actually the clandestine apprentice of the Sith lord Darth Sidious - who was none other than Supreme Chancellor Palpatine himself. The only reason the crisis had become as bad as it did and reached the point of military conflict is because of Sith manipulations: Palpatine keeping the attempts at Senate reform ineffectual (even as he feigned supporting the reformers and diplomacy), while Dooku organized the malcontents of the galaxy (who had the industrial means to produce their own armies) into an actual secessionist state. The true goal that Palpatine intended for the Separatist movement was to engineer a crisis to frighten the Republic Senate into voting him emergency powers as Chancellor, and justify a massive military buildup of a new Grand Army of the Republic - which he could later use against the Senate and the Jedi to assume truly dictatorial power.
The Clone Wars
The Clone Wars began at the Battle of Geonosis, after the Jedi Obi-Wan Kenobi and Anakin Skywalker stumbled onto gathering of Separatist leaders which formally established the Confederacy, as well as discovering the large new battle droid army being produced on the planet.
In the lead-up to this, Kenobi had also discovered a secret army of clones being produced on the distant fringe world Kamino - apparently built at the order of the Jedi and the Republic themselves. Unsure of the exact cause of their origin but in desperate need of a standing army at news of the Separatist military buildup, the Galactic Senate was convinced to vote Palpatine emergency powers, and he declared that the creation of a new Grand Army of the Republic, with the Clone Troopers as its new backbone.
The Clone Trooper army launched a massive assault on the Separatists and their droid army on Geonosis, getting in a first strike before the Separatists could do the same to them. Though the Republic forces won the day, many Jedi were killed, and worse, Dooku and the Separatist Council escaped, rallying thousands more worlds to their side who were uncommitted before they knew of the Separatists' new military might.
Ultimately the war climaxed in the Battle of Coruscant, a massive sneak attack against the Republic's capital world led by Count Dooku and General Grievous. The battle was a calculated gamble by the Confederacy but it ended in failure: not only was much of their fleet destroyed, but Count Dooku himself was killed in a lightsaber duel aboard his ship with Anakin Skywalker.
Grievous and the Separatist Council retreated to Utapau, but were followed by Kenobi leading another army group of Clone Troopers. There Grievous was himself killed in a duel with Kenobi, but just after he had already arranged to send the Separatist Council to a more secure location on the planet Mustafar, where they continued to direct droid armies across the galaxy. After Dooku's death Grievous briefly became leader of all Separatist forces, but after he also died not long afterwards, the Trade Federation's Nute Gunray briefly become leader.
The entire rise of the Separatists and the outbreak of the Clone Wars had been nothing but a ploy by Darth Sidious/Chancellor Palpatine, however, to trick the Senate into giving him dictatorial powers. With Dooku and Grievous dead, the Separatists had outlived their usefulness to him. Moreover, immediately after Grievous's death the Jedi order became aware of his true Sith identity, leading Palpatine to launch Order 66 - a secret command programmed into every Clone Trooper via an organic chip in their brains to kill their own Jedi commanders across the entire galaxy. Meanwhile, he also turned Anakin Skywalker to the Dark Side as his new apprentice Darth Vader. Thinking that Sidious was still on their side, the Separatist Council welcomed his new apprentice Vader into the heart of their command center on Mustafar - where he promptly massacred all of the Separatist leaders single-handedly, then used the equipment in their command center to send a shut-down order to every droid army still fighting a losing war across the galaxy, bringing the conflict to an abrupt end.
When the Clone Wars ended with the abrupt shut-down of the battle droid forces which made up most of their military (which was already suffering major defeats), and their core leadership destroyed, most remaining Separatist forces were either quickly overwhelmed or simply surrendered rather than face their obvious annihilation.
Some Separatist holdout worlds, however, refused to surrender, but were mostly crushed in campaigns of the awesome military force of the new Galactic Empire led by Darth Vader. After a few early years spend grinding down these holdouts the Empire's reign over the galaxy was left undisputed.
Some Confederacy member worlds were made an example of after the war: Geonosis in particular was devastated by the Empire, which apparently used some sort of biological weapon to sterilize all of the Genosians' hive queens. By about 16 years after the end of the Clone Wars, the surface of Genosis was left totally uninhabited.
By about 15 years after the fall of the Confederacy and creation of the Empire, a handful of scattered Separatist holdouts still survived here and there throughout the galaxy as local militias and insurgencies, several of which gradually merged into the wider rebellion against the Empire - even though the core leadership of the rebellion were actually pro-Republic Senators during the Clone Wars, who nonetheless opposed the tyrannical rise of the Empire.
Member worlds and factions
The core membership of the Separatist Alliance were primarily commerce guild mega-corporations that controlled entire planets as functional governments. These great engines of industry and commerce were courted by the Separatist movement because they had the most resources capable of independently producing their own armies and fleets to challenge the Republic. Many planets and races also joined the Separatists because they legitimately believed that the Republic had grown corrupt, while others were just acting out longstanding local grievances.
Some planetary populations were divided, however, in many cases leading to two rival governments fighting each other - one loyal to the Republic, one siding with the Separatists - each claiming to be the "legitimate" one. This resulted in localized proxy wars for the entire conflict. These were not always evenly divided: each side at times also attempted to prop up puppet regimes over larger populations which opposed them.
- Mandalore (Death Watch pro-Separatist faction, opposed by pro-Republic faction)
- Commerce Guilds:
- General Grievous (deceased)
- Separatist Droid Army
- Super Tactical Droid
- Kalani, a Super Tactical Droid general (active)
This list includes only points at which either "Separatist" forces were mentioned by name, or Separatist characters appeared, rather than any mention of the Clone Wars.