The Clone Wars raged across the Star Wars galaxy for over three years, and nobody could claim victory in the end despite the struggle of all parties involved. The Jedi served the Republic in their fight against Count Dooku's Separatists, with Palpatine manipulating both sides throughout the conflict. The war officially ended when Obi-Wan Kenobi defeated General Grievous, and Palpatine seized the opportunity to destroy the Jedi Order and declare that the Republic was now an Empire. While different parties may have succeeded in achieving specific goals, this doesn't mean that anybody really won the Clone Wars.
The fact neither side really triumphed at the end of the Clone Wars sets the Star Wars prequel trilogy apart from other war stories. Most conflicts, both real and fictional, end with an official declaration of who won the war, and the Star Wars franchise has often followed this pattern. The original trilogy ended with the Rebel Alliance defeating the Empire, and the sequel trilogy ended with the Resistance defeating both the First Order and Palpatine's Final Order. Even though the Clone Wars would seem to have a victor at first glance, the truth is that no person, army, or government actually won at all.
Both The Separatists & Republic Lost The Clone Wars
The Republic and the Separatists were manipulated into fighting the many battles of the Clone Wars, and both sides ended up losing. It seemed the Republic claimed victory after the Separatist council was killed, and their droid armies were shut down. However, at the same time Anakin Skywalker was killing the Separatists, Palpatine was declaring the Republic a newly formed Galactic Empire. The skeleton of the Republic may have been intact, but its ideals of freedom and democracy had been abandoned, confirming Pé's prediction that the Republic had become the very evil it was fighting to destroy.
Those loyal to the ideals of the Republic and the Confederacy of Independent Systems would continue to be punished after the end of the Clone Wars. Saw Gerrera's rebel cell, the Partisans, fought alongside the Republic in the war but refused to fight for an Empire, so iral Tarkin sent a squad to execute the soldiers left on Onderon. The Separatists fared even worse, as much of the galaxy held them responsible for the war, and any Separatist planet that refused to fall in line was severely punished. The Separatists and the Republic both set out to destroy one another, but ultimately they were both broken by the Clone Wars.
Clone Troopers Were Discarded After The Clone Wars Ended
The droid army may have been shut down, but the clone troopers were eventually discarded after the Clone Wars as well. With the galaxy-wide conflict at an end, iral Tarkin didn't believe that the clone army was worth the cost anymore, and so the Empire began phasing out clone soldiers. The fate of the Clone Army was sealed when the Empire destroyed Kamino's cloning facility, meaning no new clone soldiers would be bred for the Empire. The clones who did remain in service had to decide whether to conform to the Empire's brutality or to go AWOL and spend their lives on the run.
Life after military service in the Clone Wars was not an easy one for most clone troopers, which Captain Rex had predicted in Star Wars Rebels when he claimed that neither the clones nor the droids won the Clone Wars, only the Empire.
The Clone Wars Were An Excuse To Create The Empire
The Clone Wars ended with the Republic becoming a Galactic Empire, which was Palpatine's real goal all along. He saw the growing anger throughout the Republic over the failings of the Senate and the Jedi, and knew he could use that anger to the Sith's advantage. After becoming Supreme Chancellor, Palpatine worked with Dooku to engineer a conflict between the Republic and the Separatist movement. With Palpatine and Dooku controlling both sides, they would win no matter the outcome, and could use the Clone Wars as an excuse to further their own goals.
As the leader of a new government that he created, Dooku had the freedom to use his Separatist battle droids, making him the villain to the Republic a hero to the Separatists. Palpatine gained more control over the Republic, with the Senate voting him executive powers so that he could act quickly and decisively. The Clone Wars also gave Palpatine an excuse to spread the Clone Army across the galaxy, even to worlds that weren't originally part of the Republic. Once the Separatists were defeated, and the Jedi eliminated, there was nobody to stop Palpatine from declaring himself Emperor.
Even Palpatine Didn't Truly Win Everything He Wanted
Even though Palpatine came the closest to winning the Clone Wars, he still didn't achieve everything wanted. The Clone Wars were engineered to destroy the Jedi, but some of their greatest leaders survived, which would cause a lot of trouble for Palpatine during the reign of the Empire. Worse still, Palpatine had put years of effort into turning Anakin Skywalker into Darth Vader, only for his new apprentice to be crippled and horribly scarred on Mustafar. Palpatine was so worried that Darth Vader wouldn't meet his expectations that he seriously considered finding a new apprentice instead.
Palpatine came out on top, but nobody got what they really wanted at the end of the Clone Wars. However, this is likely the point George Lucas was trying to make, illustrating how war corrupts and ultimately hurts everyone involved. This point was explored further at the end of Star Wars: The Clone Wars season 6, where Yoda comes to believe that nobody ever truly wins a war, "For in fighting the battles, the bloodshed, already lost we have." Yoda also predicted that Palpatine would eventually be defeated, which he was, confirming that in the end, nobody won Star Wars' Clone Wars at all.
