Season 6's first story arc investigates programming within Clone Troopers as a potential mechanism behind Order 66. It features Anakin Skywalker and his 501st Legion (including Tup and Fives) along with the returning character of Admiral Trench who was last seen in "Cat and Mouse". Its episodes are titled "The Unknown", "Conspiracy", "Fugitive" and "Orders" (Source: Jedi News). A clip from the arc can be found at YouTube. The entire arc will be made available to fans as "bonus content" (Source: StarWars.com). The arc is written by Katie Lucas (Source: Brent Friedman on Twitter).
The next of The Clone Wars' final episodes are "An Old Friend", "The Rise of Clovis" and "Crisis at the Heart". They re-introduce Rush Clovis as Anakin's rival for Padme's affections and feature bounty hunter Embo as an adversary. The arc is partially set on the planet Scipio, home of the Banking Clan (Source: Star Wars Insider 137). A clip from this arc was screened for fans at Star Wars Celebration VI. Airing the Young Jedi story arc on Cartoon Network pushed the Clovis arc out of Season 5. Because it did not air as a part of the show's run on Cartoon Network, it will appear alongside the other story arcs being made available as "bonus content" (Source: RebelForce Radio). The arc is written by Christian Taylor (Source: Brent Friedman on Twitter).
The following two episodes comprise a story arc titled "The Disappeared". In these episodes, Senator Jar Jar Binks must convince Jedi Master Mace Windu to aid the peoples of a planet whose religious leaders have vanished (Source: Jedi News). These episodes are written by Jonathan Rinzler (Source: Star Wars Insider 148).
In the last ever episodes of The Clone Wars, the Jedi attempt to unravel the mystery behind Master Sifo-Dyas who was thought to be dead (Source: Jedi News). These episodes are written by Christian Taylor and are titled "The Lost One", "Voices", "Destiny" and "Sacrifice" (Sources: Brent Friedman on Twitter, Jedi News). A clip from this arc was unveiled by USA Today in April of 2013. They debuted another clip in February 2014. The same arc prominently features Yoda and more closely examines the concept of Force ghosts (Sources: Matt Michnovetz on Twitter, Bombad Radio). An additional clip from the arc in which Yoda escapes from a Jedi medical center was shown to fans at Star Wars Weekends in Orlando. Dave Filoni posted concept artwork for the arc on his Facebook page.