This Star Wars: The Clone Wars article contains spoilers.
Ever since Obi-Wan Kenobi evoked its name in A New Hope as a shorthand for Anakin Skywalker’s far-off and long-ago heroic adventures, Star Wars fans have been obsessed with the Clone Wars. Clone characters appeared in various drafts for the Original Trilogy, such as in Leigh Brackett’s first draft of The Empire Strikes Back, which featured a clone named Lando, before they finally made their canon debut in Attack of the Clones.
The Prequel era brought the Clone Wars conflict to life and the TV show has meticulously detailed the various campaigns and the major players on both sides of the war. The noble heroes of the Republic and the greedy Confederacy of Independent Systems (CIS) fought for the fate of the galaxy, but neither side knew that the war was actually being manipulated by the Sith Lord Darth Sidious.
Ultimately, the end of the Clone Wars was about more than who won and who lost. Let’s break down the intricate ending of Star Wars‘ biggest galactic conflict:
The Clone Wars Ending
The end of the Clone Wars was primarily dramatized in Revenge of the Sith. The good guys (the Republic) arguably win the military victory, defeating the CIS (aka Separatists). After the Republic victory in the Battle of Coruscant, Obi-Wan Kenobi killed General Grievous on Utapau, and, after executing Count Dooku, Anakin Skywalker mopped up the rest of the Separatist leadership on Mustafar.
But George Lucas’ true intent with the Prequel Trilogy was to show that victory in war comes at a cost and that the lines between the good guys and the bad guys aren’t always so clear. In the case of the Clone Wars, the Jedi won the war for the Republic, but they unknowingly did it at the behest of the Sith Lord who planned to destroy them and the government they’d fought to protect.
What looked like a victory for the light side, in fact, showed that a military victory without the right moral underpinnings wasn’t a victory at all. As Supreme Chancellor Palpatine, Sidious used the threat of the opposing army to take emergency control of the Senate, ultimately declaring himself Emperor. The Republic became the Empire, ringing in an era of authoritarian depredation and back-room dark side dealings.
The Rise of the Empire and Order 66
So, the simple answer is the Empire and the Sith won the Clone Wars.
The Empire still had the might of the clone army and maintained its seat of power after the Clone Wars were over. With the Separatists destroyed, Palpatine could now remake the galaxy however he wanted. This “victory” ushered in decades of oppression.
The only heroes capable of opposing the Emperor were the Jedi, most of which were wiped out during Order 66, the slaughter of countless Jedi by the clone troopers they once commanded. How did the clones so easily turn against their commanders? Control chips implanted in their brains at birth prevented them from even having a choice in the matter.
What Jedi remained — Obi-Wan Kenobi, Master Yoda, Ahsoka Tano, Caleb Dume (later known as Kanan Jarrus), and others — went into hiding. Many of these exiles were later hunted down in a great purge led by Darth Vader and his dark side enforcers, the Inquisitors.
What happened to the Clones?
One question viewers often ask after viewing the Prequel Trilogy is whether all Imperial stormtroopers are clones. Even Leia’s funny line in A New Hope, “Aren’t you a little short for a stormtrooper?” could imply that all of the Empire’s soldiers are identical. But canonically, that’s not the case.
The first generation of stormtroopers were clones. No need for the Empire to waste the army it already had, after all. But according to the official website, the clones were eventually phased out: “Over time the stormtrooper ranks were filled not by clones but by recruits, trained for blind obedience and fanatical loyalty.”
What happened to the Separatists?
Darth Sidious had influenced the Separatists as much as he had the Republic. After the war, he had no more need of them. The trade groups that made up the economic backbone of the Confederacy were absorbed into the Empire, giving it a strong industrial base and quietly removing any political power these groups had over the Senate before the war.
The Legacy of The Clone Wars
What happens in the Prequels sets up everything that comes afterward, so of course its effects are felt through all three eras of Star Wars. Even when the Rebellion gains political power and reorganizes as the New Republic, it can’t hold on to all the star systems the Old Republic once had. The Empire’s victory is so complete it affects galactic politics for decades.
The canon books and comics show that some Rebel leaders didn’t adjust well to becoming the galaxy’s ruling power. Rebel leader Mon Mothma tries to preserve the Rebellion’s moral upper hand by de-escalating military conflicts and decreasing the amount of weaponry available to the fledgling New Republic, but there are those within the new senate who secretly serve what remains of the Empire and what it will eventually become: the First Order. In the end, The Force Awakens shows us how the weak New Republic is easily destroyed by Palpatine’s resurgent war machine.
Fans of the Legends timeline know that the pre-Disney canon painted the New Republic’s fate as a bit rosier. Even though there were still plenty of conflicts to be had with the Imperial Remnant, the Emperor didn’t rise to power again in any meaningful way, even after the clone fiasco in the classic Dark Empire comics. The moral underpinnings of the New Republic were explored in a different way, with a few corrupt politicians marring a government the stories generally assumed held the moral high ground.
The new canon takes a different approach, presenting Mon Mothma, Leia, Hera Syndulla, and other Rebel leaders as good people struggling to make a system that both serves the galaxy effectively and maintains ethical standards. For a time after Return of the Jedi, the spirit of the Republic returns to the galaxy but it won’t last.