Season 1 shows a wide variety of battles and adventures with Grievous and Dooku as the lead antagonists. Many of the episodes are stand-alone, but a common thread throughout the season is that the Republic and the Separatists attempt to convince various planets and races to side with them. In Season 2, the Sith resort to hiring bounty hunters and mercenaries to steal objects and intel or to assassinate targets for them. Meanwhile, the Jedi lead the Republic forces in an assault on the primary battle droid manufacturing facility. The first half of both Season 3 and Season 4 are diplomatic in nature; Season 3, in particular, has many stories that take place away from the battlefield. How different races and planets are affected by the galaxy-wide war are shown, as well as how the Republic Senate can make a bigger difference than even the Jedi Council at times. The first half of Season 3 is used mainly to make the The Clone Wars series more cohesive as these first episodes created better chronology, setting themselves in and amongst the previous two seasons' episodes. The second half of both seasons, Anakin steps a little closer to the dark side. Meanwhile, the Sith experience turmoil amongst themselves. Season 5 is unique in that it consists of 5 four-part story arcs, 3 of which center on Ahsoka's character development. Meanwhile, the Separatists gain more ground, and the story of an old villain who has returned concludes. Season 6 explores topics that are crucial in Attack of the Clones and Revenge of the Sith, namely the creation of the clones and the details behind Order 66. Chancellor Palpatine gains even more power, and Yoda delves deeper into the nature of the Force.
On December 5, 2011, a full-length feature cut of the Season 3 trilogy episodes ("Nightsisters," "Monster," and "Witches of the Mist") was released for download on iTunes as an uninterrupted movie that was previously shown at selected screenings in 2010. The three episodes were written by Katie Lucas, who had previously written the Season 1 episode "Jedi Crash" and the Season 3 episodes "Sphere of Influence" and "Assassin." A repeat of season one aired in "decoded" episode format. Each installment contained unobtrusive text windows giving supplemental information about the characters and events playing out on screen.
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