- The Clone Wars: Prelude: set right before "Ambush"
- The Clone Wars: Shakedown: set right before "Rising Malevolence"
- The Clone Wars: Procedure: set right before "Shadow of Malevolence"
- The Clone Wars: Agenda: set right before "Destroy Malevolence"
- The Clone Wars: Mouse Hunt: set right before "Rookies"
- The Clone Wars: The Fall of Falleen: set right before "Downfall of a Droid"
- The Clone Wars: Discount: set right before "Duel of the Droids"
- The Clone Wars: Departure: set right before "Bombad Jedi"
- The Clone Wars: Transfer: set right before "Cloak of Darkness"
- The Clone Wars: The Dreams of General Grievous: set right before "Lair of Grievous"
- The Clone Wars: Bait: set right before "Dooku Captured"
- The Clone Wars: Switch: set right before "The Gungan General"
- The Clone Wars: Headgames: set some time before "Jedi Crash"
- The Clone Wars: Neighbors: set during "Jedi Crash"
- The Clone Wars: Cold Snap: set right before "Trespass"
- The Clone Wars: Shadowed: set right before "The Hidden Enemy"
- The Clone Wars: The Valley: set right before "Blue Shadow Virus" and "Mystery of a Thousand Moons"
- The Clone Wars: Covetous: set before "Storm Over Ryloth"
- The Clone Wars: Curfew: set before "Innocents of Ryloth"
- The Clone Wars: The Ballad of Cham Syndulla: set before "Liberty on Ryloth"
- The Clone Wars: Invitation Only: set before "Hostage Crisis"
In the months following the end of Season One and preceding the release of Season Two, several comics were published to bridge the arc between the two seasons. They were released in multiple parts under the name Hunting the Hunters, and were set after the first season finale "Hostage Crisis." Corresponding online games were also released on StarWars.com with each installment.
- The Clone Wars: Hunting the Hunters (Part I), released with Gunship Over Florrum
- The Clone Wars: Hunting the Hunters (Part II), released with Swamp Station Sweep
- The Clone Wars: Hunting the Hunters (Part III), released with Droids Over Iego
For the television series' second season, the comic series took a new angle. Instead of weekly installments leading into the television episodes, the new web comic series, named Act on Instinct, developed into an ongoing story of its own, occasionally weaving into the television series' storylines.
- The Clone Wars: Act on Instinct
For the series' third season, the comic series continued with the characters established in Act on Instinct.
- The Clone Wars: The Valsedian Operation
- Star Wars: Tales from The Clone Wars Webcomic Collection Season 1
- Star Wars: Tales from The Clone Wars, published version at Dreams and Visions Press