The pilot episode of the new Star Wars animated series, Star Wars: The Bad Batch, shows the Empire attempting to frame insurgent groups as the new iteration of Separatists mere days after replacing the Republic. The commandos of Clone Force 99 encounter these “Separatists” on Onderon, only to find that they’re the Clone Wars-era Onderon rebels, still led by Saw Gerrera, protecting the innocents of Onderon from the Empire’s totalitarian oppression. This makes most of the Bad Batch members question their place in the Empire, and the squad chooses to let the “Separatists” live because it’s the right thing to do. Their insubordination gets them taken into custody upon their return to Kamino, and the incident provides grim insight into the state of the galaxy in the Empire’s early days.

The Clone Wars was a key component of Palpatine’s conspiracy to destroy the Jedi and take over the galaxy. As Supreme Chancellor of the Republic, he used the threat of the Separatists (which he controlled as Darth Sidious) to frighten the Republic into granting him emergency powers, which he gradually abused as the war dragged on. By the end of the Clone Wars, the Republic was nearly a military dictatorship, with the populace too desperate and the beleaguered Jedi and Clone Troopers too preoccupied to notice. When the time was right, Palpatine activated the clones’ brainwashing with Order 66, bringing the Jedi to near-extinction and clearing the war to fully transform the Republic into the authoritarian Empire.

Related: Star Wars: How Count Dooku Turned The Galaxy Against The Republic

For years, rebel cells gradually formed across the galaxy, but the populace at large was too compliant or afraid to take a stand against the Empire. As shown in Star Wars Rebels, once-Republic politicians, such as Mon Mothma and Bail Organa, helped develop these cells and bring them together to become the Rebel Alliance, a military movement that sought to overthrow the Empire and restore democracy. Early on in the Rebellion’s history, Saw Gerrera’s cell branched off from the rest of the Alliance due to his extremism. Saw’s cell became known as the Partisans, and the Empire used their brutal reputation to harm the cause of all rebels.

The Separatists In The Clone Wars

count dooku separatists council star wars attack of the clones

The Separatist Alliance was formed when over 10,000 star systems, frustrated with the Republic’s corruption, joined the charismatic Count Dooku to form a breakaway government. The Separatist planets and politicians believed themselves to be far better represented than they were under Republic rule, which was rife with corruption from corporate lobbyists. Little did they know that the Separatist Alliance was even more corrupt than the Republic, with a council of the galaxy’s most unscrupulous megacorporations holding far more power than the Separatist Parliament. Ultimately, the entire Separatist Alliance, from Dooku to the council, to the parliament, was controlled by Darth Sidious to be the perfect opponent to the Republic during the Clone Wars.

With their massive droid army, the Separatists forced the Republic to re-establish a military force to counter them. The Clone Army, also secretly created by Sidious and Dooku, was formed to support the outnumbered Jedi with Clone Troopers. For three years, Sidious and Dooku ensured that the war would escalate, justifying Palpatine’s consolidation of power. By design, the Separatists also terrified the Republic populace with brutal military leaders, such as General Grievous and Asajj Ventress, who committed numerous war crimes. Once Order 66 was issued and the Empire officially replaced the Republic, Palpatine had his new apprentice, Darth Vader, assassinate the Separatist Council, who’d outlived their usefulness. Although Separatist holdout factions survived years after the Clone Wars ended, the Empire by and large shut down the droid army and absorbed their resources. In the age of the Empire, surviving Separatists were typically executed on sight.

The Empire Calls Rebels The Separatists In The Bad Batch

Star Wars Rebels Saw Gerrera

Due to their mutations, the clone commandos of the Bad Batch were immune to the influence of their control chips, with Crosshair as the lone exception. After a live-fire training session, Admiral Tarkin, noting the squad’s unorthodox tactics and disobedience, sends them to Onderon to put down an “insurgent” group. Grand Moff Tarkin claims that they’re Separatists who wish to continue the fight against the Empire, even though the Clone Wars were over. When the Bad Batch reaches Onderon, they find neither Battle Droids nor Separatist leaders. Their targets were civilians, including children and the elderly, and the “insurgents” guarding them were Saw Gerrera and other former Republic warriors.

Related: How Padme Created The Rebellion In Revenge Of The Sith's Original Plan

Saw and his Onderon rebels had been trained by Captain Rex during the Clone Wars to rid his home planet of Separatist oppression, but once the Republic became the Empire, Saw and his followers refused to fight for an autocracy. Naturally, they fought the Empire to protect the people of Onderon from a regime as bad (if not worse) than the Separatists. The Empire responded by labeling them as “Separatists” to prevent the truth from coming out. With the Clone Wars ending so recently, this was a smart (albeit sinister) move by the Empire to turn public opinion against the Onderon freedom fighters.

Why Using "Separatists" Is So Important

Rebel Alliance leadership aboard the Home One

Although the Separatist political figures and droid army outlived their usefulness, the idea of the Separatist Alliance continued to serve Palpatine long after his coup succeeded. For many, the eventual Rebel Alliance was seen as little more than the second iteration of the Separatists, which would understandably generate skepticism towards the Rebellion’s intentions. Some Imperials, such as Colonel Shakara Nuress, saw no difference between the two factions. Nuress was a Republic Naval officer during the Clone Wars, and she infamously referred to the Rebels as Separatists during the Galactic Civil War.

Some Separatist holdout leaders, such as the Super Tactical Droid Kalani, assisted the Rebellion in battle. Other Separatist warriors, like Cassian Andor, became Rebel agents. Despite this, the Rebellion and the Separatist Alliance were irreconcilably different factions. The Separatists sought to break away from the Republic and form a new galaxy-spanning society. The Rebels wanted to restore the Republic and remove the Empire’s fascist oppression. By blurring the line between the two, the Empire made it more difficult for the Rebellion to gain support. As shown in Star Wars: The Bad Batch, the Empire attempts to repeat the “Republic vs Separatists” dynamic from the Star Wars prequels, obstructing support for Rebel movements.

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