We finally meet Darth Maul’s brother, Savage Opress, and learn the dark secrets of Dathomir. Asajj Ventress transforms from a one-note villain into a tragic anti-hero.
Anakin, Obi-Wan, and Ahsoka are pulled into a realm where the Force is personified (The Father, The Son, The Daughter). Anakin is shown his future as Darth Vader. It is trippy, biblical, and heartbreaking.
The clones become individuals. Episode 5 ("Rookies") is the season’s first masterpiece, focusing on Rex, Cody, and the newbies Hevy and Fives. The battles are large-scale, and General Grievous is a proper villain. Star Wars The Clone Wars - Season 1- 2- 3- 4- 5...
The greatest clone story ever told. The 501st is placed under a sadistic new Jedi, General Krell, who purposely gets them killed. Clones are forced to fight each other. The ending will leave you staring at the wall.
Episode 10, "The Deserter." A clone trooper has abandoned the army, started a family, and tells Rex, "I’m not a number. I’m a person." This is where the show becomes about the morality of using slave soldiers. We finally meet Darth Maul’s brother, Savage Opress,
Maul takes over Mandalore, kills Duchess Satine in front of Obi-Wan (gut-wrenching), and creates a criminal syndicate.
Ahsoka is framed for bombing the Jedi Temple. The Council, including Mace Windu, turns on her. Anakin fights to clear her name. But when they finally admit she’s innocent... she walks away. "I’m sorry, Master. But I’m not coming back." Anakin is shown his future as Darth Vader
Season 1 introduces the formula: Anakin Skywalker (now a charismatic Jedi Knight), Obi-Wan Kenobi, Ahsoka (the bratty "Snips"), Captain Rex, and the Clone Army vs. the Separatists.
Season 3 is where The Clone Wars becomes . It retroactively fixes the prequels.
The underwater Mon Cala arc (beautiful) and the slavery arc where Ahsoka loses her innocence.
May the Force be with you.