Warning! This post contains SPOILERS for Star Wars: The Bad Batch season 2, episode 3
Star Wars has confirmed that the fall of the Empire repeated the demise of the Separatist forces as seen in The Bad Batch season 2. While the Rebellion became the New Republic following the defeat of the Sith Lords and destruction of the second Death Star, the Galactic Civil War continued and culminated in the Battle of Jakku one year after the events of Return of the Jedi. Despite being seen as the decisive victory for the New Republic, the Empire persisted with the Imperial Remnant in the Outer Rim. However, the persistence of the Empire very much resembles the aftermath of the Clone Wars.
As seen in The Bad Batch season 2, it's revealed that not all the Separatists stopped fighting at the end of the Clone Wars. Some chose to continue resisting long after the Empire's reign over the galaxy had been cemented. As such, it's ironic that the Empire's end very much resembled the Separatists whom they defeated decades prior in the Star Wars continuity.
Before The Imperial Remnant, There Were The Separatist Holdouts
Most recently confirmed in The Bad Batch season 2, clone troopers serving the Empire were still being deployed to end pockets of Separatist forces despite the demise of their leaders and the orders to shut down all production of the Droid Army. Even though the Clone Wars had come to an end, the losers entrenched themselves and continued to fight, seeing no difference between the Republic that had since become the Empire. According to previous additions to the Star Wars canon, these holdouts remained loyal to the Separatist cause, though some were so far in the western reaches of the galaxy that they hadn't even realized the war had ended.
Interestingly enough, the Separatist holdouts did serve a key purpose for the Empire, existing as a legitimate threat that encouraged stormtrooper recruitment while also motivating the continued work on the Death Star, seen as the ultimate tool to force order and control over the galaxy through fear. However, it should be noted that while the Separatist holdouts were mirrored by the Imperial Remnant following the end of the Galactic Civil War, the Separatists were almost entirely annihilated by the beginning of the original trilogy. In comparison, many members of the Imperial Remnant would survive, eventually returning as the First Order of the sequel trilogy.
Did The Surviving Separatists Join The Rebel Alliance?
That being said, there are a few rare examples of Separatists who did join or were at least involved in the Rebel cause. While most of the Separatist holdouts existed as their own entities until they were eventually destroyed by the Empire, two notable characters joined the greater force of resistance. The first would be General Kalani, an advanced tactical droid with his own battalion of still-active battle droids. Encountering the Rebel Alliance's Phoenix Squadron in the Star Wars Rebels animated series, Jedi Padawan Ezra Bridger convinced Kalani that the Republic had become the Empire.
Likewise, Lux Bonteri of Onderon was the son of a Separatist senator who fought alongside the Rebellion and Saw Gerrera. Following Saw's death on Jedha, Lux eventually led a sect of Gerrera's Partisans known as the Dreamers. Calling himself The Mentor, Lux was far less aggressive than his fellow Partisans given his prior history with the Rebel Alliance in the Star Wars canon. At any rate, the concept of history repeating itself with the Separatist holdouts and the Imperial Remnant is very entertaining, and it will be exciting to see if any more Separatist resistance will be featured in the episodes of The Bad Batch still to come.