Confederacy of Independent Systems Navy

The Confederacy of Independent Systems Navy was led by the Confederate Head of State, Count Dooku, who oversaw the day-to-day operations of the entire Confederacy military, as well as the navy. The navy was additionally led by the Supreme Martial Commander of the Separatist Droid Armies General Grievous, and a handful of other officers drawn from the ranks of the government's members, including Harch Admiral Trench, Sullustan Admiral Dua Ningo, Muun Admiral Pors Tonith, and Neimoidian Captain Mar Tuuk, all of whom served under Grievous. Furthermore, the Executive Separatist Council, the legislative branch of the Confederacy, also maintained a leadership role over the government's navy throughout the war.

Initially built up from heavily armed bulk transports, the Confederacy's naval forces contracted with several manufacturing companies to create a creditable fleet of capital ships and starfighters. These companies included Pammant Docks, Free Dac Volunteers Engineering Corps, Hoersch-Kessel Drive Inc., which were responsible for constructing the navy's Providence-class Dreadnoughts, Recusant-class light destroyers, Lucrehulk-class Battleships, Munificent-class star frigates, and Subjugator-class heavy cruisers. The navy also received much of their forces from the private merchant fleets of the Trade Federation, Techno Union, InterGalactic Banking Clan, Commerce Guild, and Corporate Alliance.

Although under the banner the Confederacy, the planet's aligned with the government were responsible for defending themselves. No organizations within the government were better equipped for such responsibilities than the conglomerates that assisted in the Confederacy's creation. Several of these corporations were known to offer defense to threatened worlds that lacked native defense fleets in exchange for the rights of their planet's resources. In addition, the Separatist navy opted to forego the construction and utilization of corvettes and traditional sized frigates within their fleets, and instead focused on assembling and using larger craft.

While the Confederacy's individual member worlds were capable of providing their own spatial defense forces, employing a variety of ships and platforms, the Confederacy navy made use of relatively few starship designs. In addition, areas of starships once used as cargo holds served as hangar bays for starfighters or staging areas for battle droids and landing craft.

In addition to support of the Confederacy's efforts, the government's leader, Count Dooku, was known to encourage both piracy and privateering to harass supply lines used by the Galactic Republic. The Confederacy and its navy were known to work alongside several pirate groups, such as the Kalarba pirates, Merson pirates, Nuala Marauders, and Nuro pirates. Support of piracy from the Confederacy was largely made a delicate and secret topic, as many of the government's member worlds had suffered from pirate raids for centuries.

Regardless of his allies, Dooku agreed to deprioritize both the eradication and capture of the groups that made predominantely targeted the Republic or the Hutt Clan, and was known to purchase material stolen from the Republic. The Confederacy also openly offered letters of marque to pirates that were willing to turn privateer, which formalized their Separatist-aligned stance. Furthermore, other pirate groups, such as the Delmaasi pirates, Iridium Pirates, and Red Fury Brotherhood all signed terms with Dooku to exclusively target Republic forces.

Other groups were known to often fly sorties on behalf of the Confederacy. These groups included Tofen's Raiders, which used elite Tempest Zero starfighters across the northern territories of Separatist space, and the Nebula Raiders, who proved to be a constant problem for the Republic, as they were known to raid their supply convoys using gun tugs and Z-95 Headhunters. Additionally, Sabaoth Squadron, a mercenary band of fighter pilots with its own support ships, was instrumental in the Confederacy's early efforts that led to the opening of the war.

Throughout the course of the Clone Wars against the Republic, the Confederacy navy was made up of several fleets that fought throughout the galaxy, ranging from planetary defense fleets to orbital blockades. In orbit of the planet Serenno, the Confederacy deployed a fleet of a variety of warships to defend the home planet of Dooku. Furthermore, due to its strategic importance, the Confederacy navy deployed an armada of dreadnoughts, battleships, destroyers and frigates in the formation of a blockade overhead its capital world of Raxus Secundus. Another fleet commanded by the ST-series super tactical droid Aut-O was positioned deep within Separatist territory, and was tasked with defending an important encryption module key to a major Separatist operation during the war.

Overhead the sulfurous, cracked planet Lola Sayu, the Confederacy navy established a defense fleet in orbit in order to protect the planet. The fleet was commanded by the T-series tactical droid, Commander K2-B4 from the Lucrehulk-class Battleship, while the fleet also possessed a single Providence-class Dreadnought flanked by four Munificent-class star frigates.

The Confederacy navy also maintained an enormous fleet under the Trade Federation Home Defense Legions positioned within the Quellor sector, as well as another fleet placed under the command of Dark Acolyte Asajj Ventress. Furthermore, a group of Separatist warships served as the personal flotilla of the Head of State, Dooku, who used it on several occasions when away from Serenno. Moreover, the Confederacy navy maintained a flotilla of Bulwark-class battle cruisers, whose secret construction was overseen by Admiral Dua Ningo of the Sullustan Home Guard, which also served within the navy. The completion of the Bulwark flotilla was anticipated to be by the second year of the Clone Wars.

Furthermore, the navy also maintained several orbital blockades among their forces. These included the Christophsis blockade over the planet Christophsis commanded by Admiral Trench, the Ryloth blockade above the planet Ryloth commanded by Captain Mar Tuuk, the Felucia blockade over the planet Felucia, and the Umbara blockade over the planet Umbara.

In addition to their fleets, the Confederacy navy also made use of starfighter squadrons. Stationed aboard the modified core ship-turned-listening post Skytop Station was the 88th Flight, a flight that consisted of Vulture-class droid starfighters. During the Battle of Sullust, the Dark Acolyte Asajj Ventress was given command over two groups of droid tri-fighters that served within the navy.

The Confederacy navy also had other units among their forces. These forces included the Grievous Legion, a Separatist battle group that made use of vulture droids, and a contingent of vulture droids located in the Corvair sector.

While the navy often employed ST-series super tactical droids, T-series tactical droids, and OOM command battle droids, of which were capable commanding their star fleets, the Confederacy also made use of organic commanders. These commanders included the elderly Sullustan Admiral Dua Ningo of the Sullustan Home Guard, a stalwart Separatist who was charged with overseeing the construction of a secret flotilla of battlecruisers, and the financier-turned-admiral Pors Tonith, an arrogant, yet well-founded Muun who had maintained strong ties with the InterGalactic Banking Clan. Another commander who joined the Confederacy navy was the Harch Admiral Trench, a legendary officer once thought dead at the Battle of Malastare Narrows and who initially assisted the Separatists in secret.

As a result of the predominant use of droid crews for the Separatist fleet, space typically required foodstuffs, water, breathable air, and quarters for an organic crew, but was made largely unnecessary and freed up design options. Such droid crews were capable of being quickly assembled and assigned to a designated starship.

These droid crews were often composed of B1-series battle droids and OOM pilot battle droids stationed aboard the command bridge of a starship. OOM-series security droids were also stationed aboard Separatist warships to maintain security. Within the starships, the Confederacy used firefighter battle droids equipped with enhanced heat shielding to eliminate any fires occurring aboard the vessel. However, despite the prevalent utilization of droids, the Confederacy was known to make use of an organic crew, sometimes consisting of Neimoidians.

The Confederacy navy adopted several different pieces of equipment for those that served within their ranks. Battle droids, such as B1-series battle droids and OOM pilot droids were often armed with E-5 blaster rifles and carried comlink booster packs, while Separatist commanders adorned white and grey uniforms and were given a single blaster pistol for protection. B1-series rocket battle droids of the navy were equipped with fusioncutters and rocket packs.

Within the navy, the Confederacy had its own rank hierarchy. The rank of Admiral was used, and were given command over entire fleet groups. Additionally, the Confederacy navy incorporated the rank of Commander, of which its rank holders were tasked with serving multiple roles, such as fleet and troop command, overseeing tactical squads and coordinating surgical strikes, while simultaneously dealing with both logistics and the politics of the Confederacy. These commanders were required to adapt to both their enemies and allies. The navy also incorporated the rank of Captain.

Despite the use of battle droids and droid starfighters among their forces, the Confederacy navy often employed organic fighter pilots. These fighter pilots often came from planets like Valahari, which was famous for its native starfighter aces and engineers.

Over the course of the war, the Confederacy navy employed several space stations among their forces. Such stations included the automated vulture droid deployment station, which was used to automatically send out a group of six Vulture-class droid starfighters towards an incoming enemy. Additionally, the navy also made use of battlespheres, former Trade Federation core ships modified with large antennae to be used as listening posts for the purpose of spying on Republic Navy operations and transmissions.

Throughout its history, the Confederacy navy utilized a variety of different types of capital ships. Dreadnoughts such as the Providence-class Dreadnoughts were one of the three most common capital ship classes used within the navy, but were deployed by the Separatist admiralty sparingly as a result of their importance and high operating cost. One variant was the Providence-class Carrier.

The navy also employed heavy cruisers, including the Subjugator-class heavy cruiser, which was equally identified as a Star Dreadnought due to its size. During the war, the navy maintained a small number of Subjugators, including the Malevolence, which served as the initial testbed and lead ship of the class. These heavy cruisers were the navy's largest warships and were larger than most of the Republic's fielded starships, and was capable of destroying entire fleets.

In addition, the Confederacy navy fielded Lucrehulk-class Battleships, which were modified Lucrehulk-class LH-3210 cargo freighters provided by the Trade Federation fleet, and served as the premier capital ship of the Separatist fleet. Furthermore, the navy employed Bulwark-class battle cruisers, a class of battlecruiser that was manufactured and deployed by the fleet during the war. Core ships, detached modules of Lucrehulk vessels, were additionally deployed by the navy, and were capable of landing on the surface to serve as ground bases. Moreover, Dual Hemisphere-Omni Support Vessels manufactured by Hoersch-Kessel Drive Inc. from salvaged Federation core ships were used to ferry spare parts and weaponry to fleet as needed.

The Separatist armada also deployed other classes of capital ships throughout the war. Such classes included the Recusant-class light destroyer, another of the most common ships used within the navy. Another type of destroyer used by the Separatists' naval forces was the Fantail-class destroyer. Additionally, a cruiser within the navy was the Diamond-class cruiser, which was provided by the Corporate Alliance.

In addition, the Munificent-class star frigate, although a frigate, was commonly used and referred to as a "pocket cruiser." A variant of the Munificent-class frigate, the Munificent-class C3 Frigate was similarly deployed, and was used for command, control, and communications roles. Provided by the Umbaran Militia, were Umbaran support ships. The Separatists have been stolen and hijacked the Venator-class Star Destroyer, and stolen the Charger c70 retrofitted Consular-class cruiser.

Sub-capital ships were also widely used within the Confederacy navy. The Trident-class assault ship, which the Confederacy equally used as aquatic gunships, was specially used. Near the end of the war, the navy began to induct modified Gozanti-class cruisers into their fleets, as well as C-ROC Gozanti-class cruisers for privateering groups.

Furthermore, Hardcell-class interstellar transports were deployed by the Confederacy naval forces as de promptu corvettes, along with its battle refit variant. These "corvettes" helped to supplement the Confederacy's Commerce Guild corvettes. C-9979 landing craft were also used by the navy to transport the Separatist Droid Army down to the surface of planets.

Lighter craft within the Separatist fleet included freighters, shuttles, transports and gunships, which were widely used throughout the war. During the war, at least one YV-865 Aurore-class freighter served in the Confederacy, while bulk transports built up a major portion of the Separatist navy early in its history.

The Separatists' complement of shuttles and other transports was vast and various. The navy also made use of HMP droid gunships, Settie-class drop ships and Separatist drop ships, Shekelesh-class freight gunships Droch-class boarding ships, H-2 executive shuttles, Maxillipede shuttles, Separatist command shuttles, Sheathipede-class transport shuttles, and Sheathipede-class Type B shuttles. The Separatists have stolen the Rho-class transport shuttle.

The Confederacy navy also utilized various types of starfighters and bombers in their fleets. However, the navy favored the use of the Variable Geometry Self-Propelled Battle Droid, Mark I, otherwise known as the Vulture-class droid starfighter, which could serve as both a starfighter and infantry support walker. The Hyena-class Droid Bomber also used a similar design language to the vulture droid, and was designed to target capital ships and fortified bases. In addition, the Separatist fleet incorporated droid tri-fighters, prototype droid starfighters that carried homing missiles and Pistoeka sabotage droids. The droid tri-fighter was also designed to replace the Vulture-class and be more threatening to Jedi pilots.

The navy also made use of Rogue-class Porax-38 starfighters, Ginivex-class fanblade starfighters, and NovaSwords, which were expensive fighters used by the Confederacy's aces. However, some aces in the Confederacy navy used their personalized craft. The Nantex-class territorial starfighter, Zenuas 33 Umbaran starfighters, Scarab-class starfighter, the Tempest Zero starfighter, and at least one Star Courier, the Scimitar, were also used in the navy.

By 22 BBY, growing dissappointment with the corrupt Galactic Republic began to create turmoil within the Galactic Senate, which led to thousands of star systems seceding from the Republic. As a result, a secessionist movement rallied under the oversight of former Jedi Master Count Dooku began. Following failed attempts on the life of Senator Padmé Amidala, Jedi Knight Obi-Wan Kenobi discovered that Dooku's Confederacy of Independent Systems were forming a secret Droid Army on the planet Geonosis while investigating the bounty hunter, Jango Fett. While on Geonosis, Kenobi further discovered that there was a large and unusual concentration of Trade Federation core ships on the surface, which had disconnected from a fleet of Lucrehulk-class Battleships in orbit.

Initially, the Confederacy navy was comprised of heavily armed bulk transports used and provided by member corporations to move their wares across the galaxy, which included the Commerce Guild, Corporate Alliance, InterGalactic Banking Clan, Techno Union, and the Trade Federation. However, after the Clone Wars erupted on Geonosis, the Separatists contracted with several shipbuilding corporations, such as Pammant Docks and other allies, to construct capital ships to make a creditable fleet. These starships also included a variety of starfighters and were crewed by B1-series battle droids.

During the war's early stages, the Confederacy launched an invasion on the planet Christophsis for its resources and strategic position along the Corellian Run hyperspace route. As a result, the Confederacy established a blockade of thirty warships in the planet's orbit under the command of Admiral Trench. In response, the Republic dispatched the task force of Jedi General Anakin Skywalker to break through the blockade and bring relief supplies to the clone forces of Senator Bail Organa, who was trapped on the surface as a result of the blockade.

However, the Republic fleet was forced to retreat to behind the planet's moon at the behest of Jedi General Kenobi, where they would recuperate. Returning to the blockade, although under orders to continue the relief mission, Skywalker flew past the blockade in a prototype stealth ship, but after Trench ordered a bombing run on Organa on the surface, Skywalker decided to go on the offensive and fight back against the blockade, resulting in the destruction of the Providence-class Dreadnought Invincible, the command ship. Despite breaking through, the Separatist fleet returned and forced the Republic warships out of the system, until they received additional reinforcements from the fleet of Republic Admiral Wurtz.

Sometime later, a Separatist fleet was sent to blockade the Twi'lek homeworld of Ryloth. The Ryloth blockade was able to cut off any form of support for the dwindling Republic fleet commanded by Admiral Dao in orbit, and the Outer Rim garrison and starving Twi'lek population below. As a result, the Republic requested Senator Organa and Junior Representative Jar Jar Binks to travel to the planet Toydaria, where they were to convince the Toydarian King, Katuunko, to allow the Republic to use the Toydarian homeworld as a staging area for relief supplies to be sent to Ryloth.

As the war prolonged, the Confederacy then deployed the first of their new Subjugator-class heavy cruiser warship, Malevolence, a dreadnought equipped with two large mega-ion cannons powerful enough to disable all power of entire fleets. Constructed by starship designer Ruggle Schmong, the Malevolence, under the command of General Grievous, used its ring-shaped ion cannons to destroy dozens of Republic fleets in attacks that left no survivors. As a result, Jedi General Plo Koon dispatched a task force of three Venator-class Star Destroyers to locate and destroy the vessel before it could carry out another strike. However, while moving through the galaxy's Phu system, the task force was intercepted by the Malevolence, resulting in its destruction.

After the attack in the Phu system, Koon and his fleet managed to track the dreadnought to the Abregado system. Aboard his Venator-class Star Destroyer, Triumphant, Koon attempted to call for Republic reinforcements, but their communications were jammed by the Malevolence, which proceeded to fire its ion cannon at Koon's entire fleet, disabling all three Star Destroyers. Shortly thereafter, the dreadnought unleashed a barrage of turbolaser fire from its hundreds of cannons, resulting in the destruction of Koon's fleet. However, Koon managed to survive his fleet's destruction and the Separatists' hunt for survivors thanks to the help of General Skywalker and his Padawan, Ahsoka Tano, allowing for the Republic to learn of the Malevolence.

Despite the Republic learning of its specifics, the Malevolence continued to launch assault on Republic fleets. One such strike was in the Ryndellia system, where it ambushed a Republic medical convoy of three Pelta-class frigates escorted by a lone Venator-class Star Destroyer. After the convoy's destruction, Dooku proceeded to task Grievous with destroying the Republic's secret Outer Rim medical station, which had been caring for 60,000 wounded clone troopers of the Republic army. In response, General Skywalker and his Padawan Tano helped to defend the station from the dreadnought with the BTL-B Y-wing starfighter/bombers of Shadow Squadron. During the defense, Shadow Squadron, despite taking heavy casualties from the dreadnought's many turbolasers and ion cannon, managed to cause heavy damage to the entire Malevolence by striking its mega-ion cannon with proton torpedoes. After dealing damage to the entire warship, Republic ships entered the system and proceeded to open fire on the Malevolence as it left for Separatist space.

As the Republic pursued the Malevolence, Dooku and his master, Darth Sidious, arranged a trap for Republic Senator Amidala to rendezvous with the warship, which she had believed was a meeting with Banking Clan representatives. As Amidala arrived, the warship brought her aboard and Grievous attempted to take her and C-3PO hostage, but they instead managed to escape further into the ship to remain undetected. Responding to Amidala's capture, Skywalker, Kenobi and R2-D2 undertook a rescue mission and infiltrated the Malevolence. While aboard, Skywalker managed to rig the dreadnought's navigation computer to force the warship to crash into the nearby Dead Moon of Antar. As a result of the Malevolences destruction, Grievous's credibility was dealt a blow and Dooku began to lose faith in his ability to lead as the Supreme Martial Commander of the Separatist Droid Armies. In addition, forces led by Jedi General Luminara Unduli intercepted a Separatist fleet sent to reinforce the Malevolence prior to its destruction.

Sometime later in the war, the Confederacy droid forces attempted to infiltrate and take control of the Republic's listening outpost on the Rishi Moon, in hopes of sabotaging its all-clear signal. The sabotaging of the signal would therefore allow a Separatist fleet of Munificent-class star frigates and Lucrehulk-class Battleships commanded by Grievous could launch an undetected attack on the planet Kamino in order to destroy the cloning facilities of Tipoca City. However, the detachment stationed at the base destroyed the station, which deactivated the hijacked all-clear signal and alerted a Republic fleet to the Rishi system, forcing Grievous and his fleet to withdraw and forfeit their plan.

Later, Grievous used another fleet of five Munificents to launch a series of attacks against Republic forces throughout the galaxy, leading him and his fleet to the planet Bothawui. After arriving at Bothawui, the Separatist fleet, alerted by the presence of a Republic fleet led by General Skywalker positioned beyond the planet's asteroid field, advanced on its opposers through the field. Coming into range of the Republic warships, Grievous ordered his frigates to open fire, disabling one of the warships in the process, forcing Skywalker to engage. As their numbers dropped from both Skywalker's Gold Squadron and force of All Terrain Tactical Enforcers spread throughout the asteroid field, Grievous's fleet was destroyed, forcing the Kaleesh to retreat.

A fleet of Separatist Munificent-class star frigates under the T-series military strategic analysis and tactics droid TF-1726 later clashed with a fleet of three Venator-class Star Destroyers under Jedi General Aayla Secura above the planet Quell. Republic reinforcements under General Skywalker came to General Secura's rescue and rescued Secura from her stricken Star Destroyer. They escaped to the planet Maridun where they encountered a Lurmen village.

In 21 BBY, the Separatist navy blockaded the planet Felucia during the First Battle of Felucia, trapping Republic forces under Jedi Generals Kenobi and Skywalker. Republic reinforcements under Jedi General Plo Koon managed to break through the blockade and evacuate Republic forces on Felucia. After stealing a holocron from the Jedi Temple on Coruscant, the Separatist-aligned bounty hunter Cad Bane's fleet of Munificent-class star frigates attacked the Republic outpost on Devaron, capturing Jedi Master Bolla Ropal. Bane wanted to use Ropal to unlock the holocron he had stolen and access its secrets. Republic reinforcements under General Skywalker and Admiral Yularen boarded Bane's flagship and destroyed his fleet. However, Bane was able to escape with the holocron and a kyber memory crystal containing a list of all the Force-sensitive children in the galaxy.

Later, a fleet led General Grievous attacked Jedi Master Eeth Koth's Venator-class Star Destroyer and captured him. In response, Jedi Generals Kenobi and Adi Gallia led a fleet of Republic warships which destroyed most of Grievous' fleet. Republic and Jedi forces then pursued Grievous on Saleucami but the Separatist droid general managed to escape off-world.

General Grievous later commanded a Separatist fleet during an assault on the planet Kamino, the homeworld of all clone troopers in the Grand Army of the Republic and their place of creation. During the battle, Grievous utilized a strategy where the fleet's transports would be sacrificed in order to protect his flagship, as the transports secretly contained pieces for Grievous's second-in-command, Asajj Ventress, to assemble into Trident-class assault ships. Upon landing, they were reassembled by Aqua droids and used to attack the clone factories on Tipoca City. Ventress attempted to steal a DNA sample of Jango Fett but was thwarted by Skywalker. The clone troopers succeeded in repelling the Separatist invaders.

A Separatist fleet under the command of Asajj Ventress and the tactical droid TJ-912 later fought against a Republic fleet led by Generals Kenobi and Skywalker, and Admiral Yularen above the planet Sullust. During the battle, the droid tri-fighter squadrons Trident group one and Trident group two destroyed the Venator-class Star Destroyer Resolute. In the midst of the battle, Darth Sidious contacted Count Dooku and ordered him to eliminate Ventress, believing that Dooku was training her as a Sith apprentice. To prove his allegiance, Dooku complied and ordered TJ-912 to bombard Ventress' Providence-class Dreadnought. Despite the bombardment, Ventress survived and became a formidable enemy of the Sith. Dooku then ordered TJ-912 to retreat from Sullust.

Later, Separatist forces ambushed Jedi General Even Piell's Venator-class Star Destroyer along the Nexus Route, which straddled the heart of both Separatist and Republic space. In response to Piell's capture, the Jedi Order and Republic mounted a mission to rescue him from the Citadel prison on Lola Sayu.

Separatist warships under General Grievous later ambushed Jedi General Adi Gallia and the 91st Mobile Reconnaissance Corps's Venator-class Star Destroyer near the planet Patitite Pattuna. Grievous' forces boarded Gallia's Star Destroyer and captured the Jedi Master. Gallia was later rescued from Grievous' flagship by a Republic fleet under Koon and Wolffe.

During the Battle of Umbara, a Separatist fleet supported the Umbaran Militia against Republic forces. The Umbarans were being supplied by a DH-Omni Support Vessel that was being protected by the Separatist fleet. The clone troopers Fives, Jesse, and Hardcase destroyed the Separatist supply ship using stolen Zenuas 33 Umbaran starfighters. This helped turn the tide of the battle in favor of the Republic. During the Battle of Dathomir, a Separatist fleet transported Separatist droid forces under Count Dooku and General Grievous to the planet Dathomir, the homeworld of the Nightsisters. All the Nightsisters with the exception of Ventress and Mother Talzin were killed during the Separatist assault.

Later, Separatist warships under General Grievous attacked General Kenobi's fleet, inflicting numerous casualties. General Kenobi managed to activate the self-destruct mechanism on the Venator-class Star Destroyer Negotiator. The explosion wiped out Grievous' landing party and at least one Munificent-class star frigate. The Republic Colonel Meebur Gascon and the droid D-Squad including R2-D2 later undertook a successful mission to steal an encryption module from the tactical droid Aut-O's flagship in Separatist space.

During a mission, Skywalker steered the T-6 shuttle that he, Senator Amidala, and Tano were traveling on into the path of a Separatist fleet. Following a brief skirmish, the trio managed to escape due to a combination of Skywalker's piloting skills and Amidala and Tano manning the shuttle's cannons.

During the last stages of the Clone Wars, the planet Cato Neimoidia, which housed the headquarters of the Trade Federation, was invaded by a Separatist fleet. Despite the planet's ties to the Separatists, the Galactic Republic authorized a defense of the Neimoidian Purse World and dispatched reinforcements under General Skywalker and Commander Tano. While the Separatist fleet clashed with Republic warships in orbit, Skywalker and Tano clashed with Separatist droid tri-fighters before being recalled to Coruscant to investigate the Bombing of the Jedi Temple hangar. Republic and Separatist forces would continue fighting until the last days of the Clone Wars.

Later, Separatist naval forces under Admiral Trench defended a space station above the planet Ringo Vinda against Jedi and Republic forces led by General Skywalker, and Masters Tiplar and Tiplee. During the battle, the Clone trooper Tup's inhibitor chip malfunctioned and he killed Master Tiplar. Upon seeing footage of "Tup" killing Tiplar, Trench attempted to kidnap the Clone trooper but Skywalker and the Clone troopers Rex and Fives managed to evacuate Tup to Kamino for medical examination.

After Rush Clovis assumed control of the InterGalactic Banking Clan, Count Dooku pressured him to raise interest rates on the Republic's loans to keep the bank afloat. Shortly later, a Separatist fleet attacked the Banking Clan's headquarters on the planet Scipio, wiping out a small Republic contingent led by Commander Thorn that had been assigned to guard Senator Amidala. In response, the Galactic Republic dispatched a fleet to take over the financial sector. Following the events on Scipio, the banks were placed under the authority of Supreme Chancellor Palpatine. Unknown to everyone else but Sidious' apprentice Count Dooku, the events on Scipio were part of a Sith plot for Palpatine's alter ego Darth Sidious to consolidate his control over the galaxy.

Following a mission to Utapau to excavate a large kyber crystal, a Separatist fleet escorted the Separatist supply ship that was to transport the kyber crystal back to Serenno. However, Generals Kenobi and Skywalker managed to infiltrate the Separatist supply ship and destroy the kyber crystal; creating an explosion that destroyed much of the Separatist fleet above Utapau. The Jedi escaped aboard a Neimoidian shuttle while Grievous escaped aboard his Belbullab-22 heavy starfighter Soulless One.

Separatist space and ground forces under Admiral Trench subsequently besieged the Republic world of Anaxes, which was the site of main production facility for the Republic Navy. Trench was aided by the captured, unconscious Republic ARC trooper Echo, who was used by Techno Union Foreman Wat Tambor to relay Rex's battle strategy algorithm to the Separatist commander. This enabled Separatist forces to make inroads against the Republic defenders. After General Skywalker, Rex, and Clone Force 99 rescued Echo from Wat Tambor, the clones managed to infiltrate Trench's flagship and shut down the droid army while General Skywalker killed Admiral Trench. After escaping, clone commando Wrecker destroyed Trench's flagship and the surrounding Separatist fleet with a remote detonator; turning the Anaxes campaign in favor of the Republic.

Later, Separatist forces under Count Dooku attacked the Mahran homeworld of Mahranee, overwhelming Republic reinforcements led by Jedi General Chubor. Separatist and Republic warships clashed in space. To punish the Mahranee for siding with the Republic, Dooku ordered his fleet to bombard General Chubor's Republic frigate and several ships carrying Mahran refugees. In addition, the Separatist leader initiated a genocide against the Mahran species. Dooku's actions led the Jedi High Council to send Master Quinlan Vos and the former Sith assassin on a mission to assassinate the Separatist leader. However, Dooku proved too powerful for the two assassins and captured Vos.

After the Death Watch rescued Darth Maul from the Spire prison on Stygeon Prime, General Grievous led a Separatist fleet in pursuit of Maul and tracked him down to the planet Zanbar. During the battle above and on Ord Mantell's surface, Maul's Shadow Collective forces ambushed the Separatist fleet and captured both Dooku and General Grievous. However, Dooku and Grievous escaped Maul's captivity due to the intervention of Darth Sidious. Grievous killed Maul's mentor Mother Talzin. Maul managed to escape but his Shadow Collective forces were scattered and eliminated as a threat to Sidious' plans for galactic domination.

Following a period of prolonged torture, Dooku managed to turn Quinlan to the dark side of the Force by revealing that Ventress had murdered his late Master Tholme. For the next several months, Vos became Dooku's new right-hand man in the Separatist hierarchy and gained the nickname "Admiral" Enigma. The Jedi Order enlisted Ventress' help in rescuing Quinlan in exchange for a pardon for her crimes against the Jedi and Republic. However, Vos had become a secret Separatist double agent as part of his quest to uncover the identity of Dooku's Sith master Darth Sidious. Despite the efforts of Vos and Ventress, Dooku escaped from Christophsis without revealing Sidious' identity; allowing the Sith Lord's plans for galactic domination to continue unhindered.

During the Outer Rim Sieges, the Separatists had been pushed back to the Outer Rim, but this kept the Republic bogged down in battles across the outer spirals. With the Jedi and Republic military scattered across the galaxy on various fronts, a large Separatist fleet led by General Grievous and Count Dooku assaulted the Republic capital of Coruscant and kidnapped Supreme Chancellor Palpatine. The Separatist fleet fought against the Republic's Open Circle Fleet. Palpatine was imprisoned aboard the Separatist flagship, the Providence-class dreadnought Invisible Hand but was rescued by Jedi Generals Skywalker and Kenobi with the help of R2-D2. At the urging of Palpatine, Skywalker slew Count Dooku, drawing the young Jedi closer to the dark side. However, Grievous escaped to Utapau to hide with the Separatist Council aboard a core ship. The Battle of Coruscant saw the destruction of a third of the Separatist fleet involved in the attack.

Following the execution of the Separatist Council at the hands of Anakin Skywalker, who had embraced the persona of Darth Vader, the Separatist navy, along with the Separatist Droid Army, was presumably deactivated and demobilized. The Galactic Republic was transformed into the Galactic Empire under the leadership of the self-appointed Emperor Palpatine. With the collapse of the Separatist leadership, Imperial forces took over many former Separatist worlds including Antar 4, Raxus Secundus, Kooriva, and Murkhana.

Many former Separatist warships including the Providence-class Dreadnought Lucid Voice were dismantled at shipyards such as Bilbringi shipyards. Despite this, former Separatist warships and weapons occasionally surfaced. In 14 BBY, the former Republic Intelligence Agent Berch Teller's rebel cell utilized a modified Providence-class Dreadnought and numerous Vulture droids and droid tri-fighters. In an attempt to undermine his rival Moff Wilhuff Tarkin, Vice Admiral Dodd Rancit had used his position as Director of the Naval Intelligence Agency and underworld connections to supply Teller's insurgents with former Separatist weapons and equipment. Tarkin and Darth Vader defeated Teller's insurgents following a brief campaign and exposed Rancit's duplicity. Other insurgent groups such as Cham Syndulla's Free Ryloth Movement and Nightswan also utilized former Separatist vulture droids and buzz droids.

As late as 2 BBY, wrecked Separatist ships could still be found in deep space. While waiting to rendezvous with former Senator Mon Mothma, the Spectres hid their starship Ghost near the wreckage of a Recusant-class light destroyer and Munificent-class star frigate.

During the Galactic Civil War, a former Trade Federation Lucrehulk-class Battleship—Lucrehulk Prime—was utilized by the Rebel Alliance, commanded by the Twi'lek general Hera Syndulla. Sometime after the destruction of the first Death Star, however, it participated in the Hivebase-1 infiltration in 0 ABY.

The Alliance Navy would also use a heavily mortified Recusant-class light destroyer and a Providence-class Dreadnought alongside other Mon Cala cruisers to battle the Imperial Navy in outer space.

The Separatist navy debuted in the 2002 episodic film, Star Wars: Episode II Attack of the Clones, and was first identified as the Separatist navy in the reference book, Ultimate Star Wars.