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.
