The Clone Wars is a special part of the Star Wars universe. While there are other shows, and, of course, it is hard to compare the series to the movies, Clone Wars is a unique piece of content with wonderful stories and characters. For seven seasons, it constantly surprised fans.
The show contains deaths, touching introductions, heartbreaking goodbyes, and shocks that totally subvert fans' expectations, many of whom assumed it might form a linear path between Attack of the Clones and Revenge of the Sith. Overall, the show is just generally filled with colossal plot twists and reveals that severely impact and improve the canon.
Anakin's Apprentice
This reveal actually comes from the lackluster The Clone Wars movie in which Ahsoka made her Star Wars debut, but it is so crucial for the series that it is included here.
When it is revealed Anakin gets an apprentice in Ahsoka, it was a surprise, to say the least. She was never mentioned in the prequels, and there was no indication Anakin had taught a Padawan. It led many to think she would end up dying, but, of course, the canon went a far more interesting route.
Vader Returns
Fast forward twelve years, and fans are being subject to the emotionally devastating Siege of Mandalore arc, with Revenge of the Sith happening simultaneously and the lives of these beloved characters changing forever.
The very last scene of "Victory and Death" sees a surprise, yet perfect, appearance from Darth Vader, who arrives at the crashed Venator site, presumably looking for Ahsoka, and wields the lightsaber he gifted her before their final goodbye. It is a painful yet beautiful scene, with the Morai, the convor attached to Ahsoka since the Daughter transferred her life essence to her, flying above.
Dooku Betrays Ventress
Both Asajj Ventress and Count Dooku are great villains throughout The Clone Wars, with the former improving so much from the prequels and the latter being a total badass with a fantastic arc.
A crucial point in the show for both characters came when Sidious told Dooku he had to kill Ventress. This betrayal was a surprise, even more so since Dooku failed, and Ventress attempted to assassinate him out of revenge before going on to become a bounty hunter and mercenary. These happenings built up to the events of Dark Disciple.
Echo Is Alive
Many a beloved clone pass through the Star Wars canon over the years, from Rex to Cody to Fives to 99 to Grey to Gregor, and more, but one standout is undoubtedly Echo.
Echo appears to meet his end during the great Citadel arc. It is definitely emotional. Fast forward to the Bad Batch arc of season 7, when Rex is sure Echo is alive and being used by the Separatists. Though some of this already played out in the unfinished reels, that itself was a surprise, and it was even more shocking to see Echo turned into a machine.
"They're Not Umbaran's; They're Clones."
Before the Siege of Mandalore came and seemed to blow everything out of the water, there were a handful of arcs fans that seemed to be undisputedly the best of The Clone Wars, with the Umbara arc being a fan favorite.
Pong Krell has sent his men out to fight Umbarans who have gotten hold of clone armor, who are in reality clones who have been told the same thing in a heartbreaking twist. Rex screaming at his brothers to stop shooting after realizing what was happening was a brilliant moment. To add further to the twist, there is a separate reveal that Pong Krell hopes to catch the attention of Dooku and become his next Sith apprentice.
Exploring The Force
One thing The Clone Wars does, which the movies in the Skywalker saga never had the capacity to do, was explore the Force in more depth.
The main shock related to these stories comes from the Mortis arc as Anakin's status as the chosen one goes under scrutiny. The two biggest reveals of this arc are that, for one, Ahsoka dies and has to come back to life with the help of the Ones and Anakin, and two that Anakin actually saw his future, he saw himself as Darth Vader, but the Father wiped his memory of those events. The other huge Force arc in the show is Yoda's, which shows how painfully close Yoda came to uncovering the truth.
The Behavioral Modification Chip
Speaking of the truth, one of the most significant questions surrounding the show as a whole is why did the clones so willfully obey Order 66? It was easy to assume it was simply because they were obeying orders, but the show depicts clones as true individuals.
In one of the most gut-wrenching arcs of the show, beloved ARC trooper Fives uncovers the truth. It was behavioral modification chips, inhibitor chips, that were programming the clones. This was one of the most significant reveals of the show, and the effects of these chips can be felt across both Rebels and The Bad Batch.
Obi-Wan & Satine
Unlike both his Master and his Apprentice, Obi-Wan Kenobi was a very obedient Jedi, someone who, while intelligent enough to disagree and have his own thoughts, fell in line with the Jedi Code and the Jedi High Council.
So when it was revealed that Obi-Wan had fallen in love, it came as a shock. The romance between Satine and Obi-Wan is one of the greatest 'what ifs' ever in Star Wars. The two are amazing together, and seeing that side of Obi-Wan and hearing of that history adds so much to his character.
Ahsoka Is Framed & Leaves The Jedi Order
Ahsoka Tano ended up becoming one of the most crucial components in Anakin Skywalker's fall to the dark side, acting as perhaps the biggest example of how he could not trust the Jedi Council.
The whole arc of Ahsoka getting framed is shocking, but two moments stick out above all else. The reveal that Barriss Offee was the one framing Ahsoka was set up throughout the arc but is still a shock the first time around. Of course, the biggest shock comes when Ahsoka refuses to rejoin the Jedi Order, leaving it behind and leaving Anakin behind.
Maul Lives
From a heartbreaking goodbye to a pretty awe-inspiring return, if there were one prequel trilogy character fans did not expect to see in The Clone Wars, it was Darth Maul.
But, with spider-legs, frantic insanity, and an insurmountable level of hatred and anger, Maul returned, no longer a Darth, and with the help of Savage and Mother Talzin, he returned to be a menace to the Galaxy. There was doubt surrounding his return for obvious reasons, but even with the silly spider-legs, the character of Maul managed to create an even greater legacy thanks to his role throughout The Clone Wars.