Summary

• The Clone Wars were orchestrated by the Sith to destroy the Jedi's legacy and reputation, not just the Jedi themselves.
• The Sith's ultimate goal was to ensure the Jedi wouldn't return by discrediting their legacy, turning survivors into fugitives rather than martyrs.
• The war made the Jedi appear as enemies of peace, leading to their downfall and the rise of the Empire, exactly as Palpatine and his master Darth Plagueis had intended (revealed in Legends' Darth Plagueis novel).

Since the dawn of the Star Wars: Episode II - Attack of the Clones, the true purpose of the galactic conflict has been missed. Orchestrated by the Sith Lords, the Clone Wars and its ultimate goals went much further in its inception beyond simply bringing about the Jedi Order's destruction. Instead, the Clone Wars were specifically engineered for the resulting aftermath as well.

Secretly controlling both sides of the three-year conflict that spanned the entire Star Wars galaxy, Darth Sidious aka Supreme Chancellor Palpatine always intended to use the Grand Army of the Republic to not only turn the existing democratic government into his very own Empire, but also to fulfill the generations-long Sith Imperative by destroying the Jedi with Order 66, finally claiming revenge in the name of the dark side. However, Legends confirms that Palpatine specifically needed the Clone Wars to play out as they did, ensuring that the aftermath played in favor of the Sith, rather than the Jedi.

The Clone Wars Were Designed To Destroy The Jedi Order's Reputation

The Death of the Jedi Order Wasn't The Only Goal

In the non-canon Legends novel Darth Plagueis by James Luceno set years before The Phantom Menace, it's revealed that Sidious and his dark Sith master intentionally sought a means to not only destroy the Jedi, but also to discredit their entire legacy along the way. However, destroying the entire Jedi Order was a hard enough task on its own. In the novel, Darth Plagueis himself notes that the Jedi couldn't be beaten even when the Sith were legion such as they were in the days of the Old Republic: “No mere army can overwhelm the Jedi”.

However, it's Sidious who suggests that the Jedi Order must not only be "lured into a trap of their own devising", but also be made to look like "the enemies of peace and justice, rather than the guardians." To that end, this is exactly what the Clone Wars does to the Jedi Order by its end. After all, the Jedi compromised their code and tenets by serving as generals of the Republic's new clone armies.

Furthermore, the Jedi then find themselves in the crosshairs of their own troopers thanks to Order 66. Before the war even began, Palpatine and Count Dooku secretly orchestrated the clones' creation, as well as their secret behavioral modification chips that forced them to turn on the Jedi.​ Following the brutal massacre of Jedi, the galaxy was made to believe that the Jedi had betrayed the Republic, generating devastating results for any surviving Jedi at the Clone Wars' end and the rise of Palpatine's Empire (just as Sidious and his late master Darth Plagueis had intended).

The Sith Didn't Just Want To Destroy The Jedi... They Wanted To Ensure They Wouldn't Return

"The Enemies of Peace and Justice"

Rather than becoming martyrs, the Jedi were made to look like enemies to the new galactic order established by the Sith. As such, the Clone Wars were the perfect vehicle to bring about this galaxy-wide perception, forcing any survivors to go into hiding as fugitives while being hunted down by agents of the Empire. Furthermore, it all transpired exactly as Palaptine envisioned when speaking with Darth Plagueis, years before he was appointed Supreme Chancellor: "The galaxy must turn its back to the light."

Even coming from non-canon Legends, the chilling notion remains that so much of the Sith's plans with the Clone Wars proceeded just as intended. However, that's not to say that the reign of Palpatine's Empire lasted given the rise of Luke Skywalker and Leia Organa as the galaxy's new hope. That said, the Sith still have to be given credit for their "Grand Plan", seeing as how the Jedi have still struggled to regain the numbers they once had in the prequels, even after the events of the sequels.