In the decades prior to the Clone Wars, the Galactic Republic was seen by many as a failing government, plagued by corruption and mindless bureaucracy that stifled the voices of many constituents represented in the Galactic Senate. Secession grew during the period following the Invasion of Naboo, and the commerce guilds and trading corporations became disillusioned with the Republic after the law was passed to place taxation on all trade routes to outlying star systems. Into this critical situation stepped Count Dooku, a former Jedi who had become disillusioned with the Republic and the Jedi Order that served it. This charismatic figure stirred up anti-Republic sentiments on many worlds, paving the way for a rebellion against the government. A loose affiliation of separatists was formed, with Dooku at their head, pushing for a new government to take the place of the stagnant Republic. Eventually, this movement established itself as the Separatist Alliance, a body formally opposed to the Galactic Republic.

The members of the Separatist movement included the Corporate Alliance, Trade Federation, Commerce Guild, InterGalactic Banking Clan and the Techno Union. Although the Republic recognized that many of its member worlds were in rebellion, it refused to formally acknowledge the existence of the Separatists as their common government, deeming that doing so would legitimize it. Unknown to the Republic, Dooku was also Darth Tyranus, apprentice to Darth Sidious, who had previous ties with the Trade Federation ordered the Invasion of Naboo. Under the guise of Supreme Chancellor Palpatine of the Republic, Sidious had used Tyranus as the public leader for the Separatists in the Sith plot to destroy the Jedi Order and transform the galaxy. The secessionist movement that began twenty-four years before the Battle of Yavin would lead to a political crisis in which tensions escalated between the newly-formed alliance and the reigning Galactic Republic.

Twenty-two years before the Battle of Yavin, 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. 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 by Darth Vader under the command of Darth Sidious. With the subsequent shutdown of the Droid Army, the organization 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 successor state of the Galactic Republic, the Galactic Empire, whether voluntarily or under threat.