The Confederacy military, also known as the Separatist military or CIS military, was the armed forces of the Confederacy of Independent Systems, comprised by various branches including the Separatist Droid Army and the Confederacy navy. The Droid Army was composed of the Techno Union Droid Army, the Trade Federation military, the Geonosian droid army, the IG-series battle droid army, the Retail Caucus droid army, and the forces of the InterGalactic Banking Clan, Corporate Alliance, and the Commerce Guild, while other worlds, systems and sectors also provided local military units.
Thirteen years before the Fall of the Republic, the Trade Federation was allowed to maintain an army of B1-series battle droids to protect valuable shipments from piracy. The first major deployment of the Trade Federation's army was during the blockade and subsequent invasion of Naboo. The army fought against both the Royal Security Forces and the Gungan Grand Army. The Trade Federation fleet was used to blockade the planet. However, the Federation military was eventually defeated, as the young Force-sensitive Anakin Skywalker destroyed the Vuutun Palaa, resulting in the battle droids shutting down.
Other conglomerates, such as the Techno Union, had their own armies to protect their interests. During the Separatist Crisis, the Techno Union, Trade Federation and the other conglomerates then pledged their armies to Count Dooku and the emerging Confederacy of Independent Systems. Together they formed the basis for the military The Retail Caucus also pledged their droid army before the Battle of Christophsis. For years before the outbreak of the Clone Wars, the Confederacy had been secretly building and training commanders.
Following a meeting on Geonosis between Dooku and his allies, the Republic learned that the Confederacy would take the shipment and use their army to force the Republic to their demands. When Jedi Master Obi-Wan Kenobi was captured, the Republic's Supreme Chancellor Palpatine was given emergency powers by the Galactic Senate to create a Grand Army of the Republic, using an army ordered by Jedi Master Sifo-Dyas. Both the Separatist Droid Army and the Republic's Grand Army fought against each other on Geonosis in the opening battle of the Clone Wars.
Despite the defeat, the Confederacy was able to seize control of the major hyperspace lanes, thus separating the Republic from the majority of its troops. The military would continue to be a effective fighting force against the Republic.
While the Republic came have more victories than losses, the droid armies under Grievous's command would win multiple victories against the Republic, such as his capture of Eeth Koth and his bombing of Coruscant's central power distribution grid. Among Grievous's most daring assaults was at the war's end when he launched an assault on Coruscant and attempted to escape with the Supreme Chancellor. However, it failed when Kenobi and Skywalker killed Dooku and rescued the Chancellor.
Following Dooku's death, Grievous became the new Head of State of the Confederacy. However, his reign was short-lived as it came to a swift end when Kenobi found and destroyed him on Utapau. The military then fell under the command of the Council. However, their time ended when Lord Sidious's new apprentice, Darth Vader eliminated them on Mustafar. Vader also transmitted a master control signal that deactivated much of the Separatist military's droid forces. The elimination of the Separatists and the Great Jedi Purge enabled Palpatine to implement his Galactic Empire with himself as Emperor.
Despite the dissolution of the Confederacy, its legacy still remained in the form of Separatist holdouts. Stormtroopers of the Empire were tasked with destroying surviving battle droids on sight. During the Imperial Era, at least three anti-Imperial insurgent groups, Cham Syndulla's Free Ryloth Movement, Berch Teller's rebel cell and Nevil Cygni made use of Separatist equipment.
In 2 BBY, the former Clone Captain Rex and members of the Spectres rebel cell encountered the super tactical droid general Kalani and his garrison of battle droids on Agamar during a salvage mission to obtain proton bombs from a derelict Separatist supply ship. Kalani had overrode the command signal on Agamar, believing it to be a Republic trick. Determined to end the Clone Wars on his terms, Kalani forced Rex and the Spectres to take part in a war game. The Jedi padawan Ezra Bridger convinced Kalani and Rex to put aside differences and make peace. The two sides then joined forces to escape an Imperial attack on Agamar.
The future New Republic and Resistance starfighter pilot Temmin Wexley also rebuilt and befriended a heavily-modified B1 battle droid named Mister Bones. Mister Bones fought during the Galactic Civil War and met his end at the Battle of Jakku.
- "The duke that Oenti mentioned. Is he the leader of the Separatists?"
"No, that's Count Dooku. The other real driving force of their military is General Grievous."
- ―Commander Thrawn and Jedi General Anakin Skywalker
As leader of the Confederacy and the Separatist Senate, Dooku held the most authority over Confederacy military operations and its strategies. Only members of the Separatist Council such as Viceroy of the Trade Federation Nute Gunray, Emir Wat Tambor, and Archduke Poggle the Lesser were known to take command of their military's various operations personally. One of the Confederacy's best officers was the Kaleesh cyborg, General Grievous, who served as Supreme Martial Commander of the Separatist Droid Armies. Under Grievous and Dooku served a number of high-ranking officers including Supreme Leader Asajj Ventress, General Kleeve, Duke Solha, and Colonel Coburn Sear.
Although primarily composed of droid forces, the Confederacy military also consisted of the armed forces of the worlds under its control. The Umbaran Militia, Zygerrian royal guards, several Kage Warriors, and Geonosians from the Stalgasin hive.
- "Separatist droid armies stomped through our cities, blasting and bombing. They seemed to have no purpose. Just to destroy things. Everything they could. […] We had an army of our own, of course, but they were beaten quickly. There seemed to be an endless supply of those robots, but not of us. Even when we stopped fighting back, the droids just kept marching and destroying."
- ―Mayvlin Trillick describes the Separatist invasion of Oktaro
The droid army was the largest army assembled during its era, reportedly outnumbering the Republic clone army by a hundred to one. The Separatist Droid Army was formed by the armies of several large corporations, including the Trade Federation Droid Army, the Techno Union Droid Army, the Retail Caucus's private droid army, the Commerce Guild's army, and the army of the Corporate Alliance. The ranks of the Separatists also included a limited number of flesh and blood soldiers, however, officials such as Count Dooku touted that these were volunteers rather than cloned soldiers which had been pressed into service.
The Confederacy of Independent Systems Navy saw early action in the Clone Wars during the Battle of Christophsis where Admiral Trench blockaded the planet and held off Republic forces until the destruction of his flagship, the Invincible. One ship in the navy, the Subjugator-class heavy cruiser Malevolence, terrorized Republic convoys early in the war, and was initially perceived as a "mystery weapon." It was eventually discovered, however, that the Malevolence was equipped with two mega-ion cannons that allowed it to leave enemy vessels defenseless with a single shot. The Malevolence was destroyed during the Battle of the Kaliida Nebula.
As well as Dooku being killed, the Separatists lost a third of its fleet during the Battle of Coruscant.
The Separatist navy was primarily composed of starships utilized by groups like the Trade Federation and the InterGalactic Banking Clan. The capital ships were also augmented by forces of starfighters, primarily composed of Vulture-class droid star fighters and Droid tri-fighters.