Star Wars: Clone Wars was an animated series that takes place largely between episodes "Attack of the Clones" (Episode II) & "Revenge of the Sith" (Episode III) (Star Wars Viewing Order). For some reason they were shown out of chronological order, causing some events to be confusing to viwers. If you want to watch in chronological order, here is the OFFICIAL list put out by Lucasfilm (link at the bottom) and split the episodes into the appropriate story arcs by myself.
The Battle of Christophsis- Season 2, Episode 16 - Cat and Mouse
- Season 1, Episode 16 - Hidden Enemy
- Star Wars: The Clone Wars (film)
- Season 3, Episode 1 - Clone Cadets
- Season 3, Episode 3 - Supply Lines
- Season 1, Episode 1 - Ambush
- Season 1, Episode 2 - Rising Malevolence
- Season 1, Episode 3 - Shadow of Malevolence
- Season 1, Episode 4 - Destroy Malevolence
- Season 1, Episode 5 - Rookies
- Season 1, Episode 6 - Downfall of a Droid
- Season 1, Episode 7 - Duel of the Droids
- Season 1, Episode 8 - Bombad Jedi
- Season 1, Episode 9 - Cloak of Darkness
- Season 1, Episode 10 - Lair of Grievous
- Season 1, Episode 11 - Dooku Captured
- Season 1, Episode 12 - The Gungan General
- Season 1, Episode 13 - Jedi Crash
- Season 1, Episode 14 - Defenders of Peace
- Season 1, Episode 15 - Trespass
- Season 1, Episode 17 - Blue Shadow Virus
- Season 1, Episode 18 - Mystery of a Thousand Moons
- Season 1, Episode 19 - Storm over Ryloth
- Season 1, Episode 20 - Innocents of Ryloth
- Season 1, Episode 21 - Liberty on Ryloth
- Season 2, Episode 1 - Holocron Heist
- Season 2, Episode 2 - Cargo of Doom
- Season 2, Episode 3 - Children of the Force
- Season 2, Episode 17 - Bounty Hunters
- Season 2, Episode 18 - The Zillo Beast
- Season 2, Episode 19 - The Zillo Beast Strikes Back
- Season 2, Episode 4 - Senate Spy
- Season 2, Episode 5 - Landing at Point Rain
- Season 2, Episode 6 - Weapons Factory
- Season 2, Episode 7 - Legacy of Terror
- Season 2, Episode 8 - Brain Invaders
- Season 2, Episode 9 - Grievous Intrigue
- Season 2, Episode 10 - The Deserter
- Season 2, Episode 11 - Lightsaber Lost
- Season 2, Episode 12 - The Mandalore Plot
- Season 2, Episode 13 - Voyage of Temptation
- Season 2, Episode 14 - Duchess of Mandalorie
- Season 2, Episode 20 - Death Trap
- Season 2, Episode 21 - R2 Come Home
- Season 2, Episode 22 - Lethal Trackdown
- Season 3, Episode 5 - Corruption
- Season 3, Episode 6 - The Academy
- Season 3, Episode 7 - Assassin
- Season 3, Episode 2 - ARC Troopers
- Season 3, Episode 4 - Sphere of Influence
- Season 3, Episode 8 - Evil Plans
- Season 1, Episode 22 - Hostage Crisis
- Season 3, Episode 9 - The Hunt for Ziro
- Season 3, Episode 10 - Heroes on Both Sides
- Season 3, Episode 11 - Pursuit of Peace
- Season 2, Episode 15 - Senate Murders
- Season 3, Episode 12 - Nightsisters
- Season 3, Episode 13 - Monster
- Season 3, Episode 14 - Witches of the Mist
- Season 3, Episode 15 - Overlords
- Season 3, Episode 16 - Altar of Mortis
- Season 3, Episode 17 - Ghosts of Mortis
- Season 3, Episode 18 - The Citadel
- Season 3, Episode 19 - Counter Attack
- Season 3, Episode 20 - Citadel Rescue
- Season 3, Episode 21 - Padawan Lost
- Season 3, Episode 22 - Wookiee Hunt
- Season 4, Episode 1 - Water War
- Season 4, Episode 2 - Gungan Attack
- Season 4, Episode 3 - Prisoners
- Season 4, Episode 4 - Shadow Warrior
- Season 4, Episode 5 - Mercy Mission
- Season 4, Episode 6 - Nomad Droids
- Season 4, Episode 7 - Darkness on Umbara
- Season 4, Episode 8 - The General
- Season 4, Episode 9 - Plan of Dissent
- Season 4, Episode 10 - Carnage of Krell
- Season 4, Episode 11 - Kidnapped
- Season 4, Episode 12 - Slaves of the Republic
- Season 4, Episode 13 - Escape from Kadavo
- Season 4, Episode 14 - A Friend in Need
- Season 4, Episode 15 - Deception
- Season 4, Episode 16 - Friends and Enemies
- Season 4, Episode 17 - The Box
- Season 4, Episode 18 - Crisis on Naboo
- Season 4, Episode 19 - Massacre
- Season 4, Episode 20 - Bounty
- Season 4, Episode 21 - Brothers
- Season 4, Episode 22 - Revenge
- Season 5, Episode 2 - A War on Two Fronts
- Season 5, Episode 3 - Front Runners
- Season 5, Episode 4 - The Soft War
- Season 5, Episode 5 - Tipping Points
- Season 5, Episode 6 - The Gathering
- Season 5, Episode 7 - A Test of Strength
- Season 5, Episode 8 - Bound for Rescue
- Season 5, Episode 9 - A Necessary Bond
- Season 5, Episode 10 - Secret Weapons
- Season 5, Episode 11 - A Sunny Day in the Void
- Season 5, Episode 12 - Missing in Action
- Season 5, Episode 13 - Point of No Return
- Season 5, Episode 1 - Revival
- Season 5, Episode 14 - Eminence
- Season 5, Episode 15 - Shades of Reason
- Season 5, Episode 16 - The Lawless
- Season 5, Episode 17 - Sabotage
- Season 5, Episode 18 - The Jedi Who Knew Too Much
- Season 5, Episode 19 - To Catch a Jedi
- Season 5, Episode 20 - The Wrong Jedi
- Season 6, Episode 1 - The Unknown
- Season 6, Episode 2 - Conspiracy
- Season 6, Episode 3 - Fugitive
- Season 6, Episode 4 - Orders
- Season 6, Episode 5 - An Old Friend
- Season 6, Episode 6 - The Rise of Clovis
- Season 6, Episode 7 - Crisis at the Heart
- Season 6, Episode 8 - The Disappeared
- Season 6, Episode 9 - The Disappeared Pt. II
- Season 6, Episode 10 - The Lost One
- Season 6, Episode 11 - Voices
- Season 6, Episode 12 - Destiny
- Season 6, Episode 13 - Sacrifice
- Unaired - A Death on Utapau
- Unaired - In Search of the Crystal
- Unaired - Crystal Crisis
- Unaired - The Big Bang
- Season 7, Episode 5 - Gone with a Trace
- Season 7, Episode 6 - Deal No Deal
- Season 7, Episode 7 - Dangerous Debt
- Season 7, Episode 8 - Together Again
- Season 7, Episode 1 - The Bad Batch
- Season 7, Episode 2 - A Distant Echo
- Season 7, Episode 3 - On the Wings of Keeradaks
- Season 7, Episode 4 - Unfinished Business
- Unaired - Lethal Alliance
- Unaired - The Mission
- Unaired - Conspirators
- Unaired - Dark Disciple
- Unaired - The Enemy of My Enemy
- Unaired - A Tale of Two Apprentices
- Unaired - Proxy War
- Unaired - Showdown on Dathomir
- Unaired - Saving Vos Part 1
- Unaired - Saving Vos Part 2
- Unaired - Traitor
- Unaired - The Path
- Season 7, Episode 9 - Old Friends Not Forgotten
- Season 7, Episode 10 - The Phantom Apprentice
- Season 7, Episode 11 - Shattered
- Season 7, Episode 12 - Victory and Death
List taken from STAR WARS: THE CLONE WARS CHRONOLOGICAL EPISODE ORDER
