Star Wars The Clone Wars was not aired in chronological order but fortunately if you want to do a huge The Clone Wars marathon, has posted the chronological order of the series including the TCW Legacy content.

Star Wars Episode II Attack of the Clones

216 Cat and Mouse
116 Hidden Enemy

T The Clone Wars theatrical release
3×01 Clone Cadets
3×03 Supply Lines
1×01 Ambush
1×02 Rising Malevolence
1×03 Shadow of Malevolence
1×04 Destroy Malevolence
1×05 Rookies
1×06 Downfall of a Droid
1×07 Duel of the Droids
1×08 Bombad Jedi
1×09 Cloak of Darkness
1×10 Lair of Grievous
1×11 Dooku Captured
1×12 The Gungan General
1×13 Jedi Crash
1×14 Defenders of Peace
1×15 Trespass
1×17 Blue Shadow Virus
1×18 Mystery of a Thousand Moons
1×19 Storm over Ryloth
1×20 Innocents of Ryloth
1×21 Liberty on Ryloth
2×01 Holocron Heist
2×02 Cargo of Doom
2×03 Children of the Force
2×17 Bounty Hunters
2×18 The Zillo Beast
2×19 The Zillo Beast Strikes Back
2×04 Senate Spy
2×05 Landing at Point Rain
2×06 Weapons Factory
2×07 Legacy of Terror
2×08 Brain Invaders
2×09 Grievous Intrigue
2×10 The Deserter
2×11 Lightsaber Lost
2×12 The Mandalore Plot
2×13 Voyage of Temptation
2×14 Duchess of Mandalore
2×20 Death Trap
2×21 R2 Come Home
2×22 Lethal Trackdown
3×05 Corruption
3×06 The Academy
3×07 Assassin
3×02 ARC Troopers
3×04 Sphere of Influence
3×08 Evil Plans
1×22 Hostage Crisis
3×09 Hunt for Ziro
3×10 Heroes on Both Side
3×11 Pursuit of Peace
2×15 Senate Murders
3×12 Nightsisters
3×13 Monster
3×14 Witches of the Mist
3×15 Overlords
3×16 Altar of Mortis
3×17 Ghosts of Mortis
3×18 The Citadel
3×19 Counter Attack
3×20 Citadel Rescue
3×21 Padawan Lost
3×22 Wookiee Hunt
4×01 Water War
4×02 Gungan Attack
4×03 Prisoners
4×04 Shadow Warrior
4×05 Mercy Mission
4×06 Nomad Droids
4×07 Darkness on Umbara
4×08 The General
4×09 Plan of Dissent
4×10 Carnage of Krell
4×11 Kidnapped
4×12 Slaves of the Republic
4×13 Escape from Kadavo
4×14 A Friend In Need
4×15 Deception
4×16 Friends and Enemies
4×17 The Box
4×18 Crisis on Naboo
4×19 Massacre
4×20 Bounty
4×21 Brothers
4×22 Revenge
5×02 A War on Two Fronts
5×03 Front Runners
5×04 The Soft War
5×05 Tipping Points
5×06 The Gathering
5×07 A Test of Strength
5×08 Bound for Rescue
5×09 A Necessary Bond
5×10 Secret Weapons
5×11 A Sunny Day in the Void
5×12 Missing in Action
5×13 Point of No Return
5×01 Revival
5×14 Eminence
5×15 Shades of Reason
5×16 The Lawless
5×17 Sabotage
5×18 The Jedi Who Knew Too Much
5×19 To Catch a Jedi
5×20 The Wrong Jedi
6×01 The Unknown
6×02 Conspiracy
6×03 Fugitive
6×04 Orders
6×05 An Old Friend
6×06 The Rise of Clovis
6×07 Crisis at the Heart
6×08 The Disappeared
6×09 The Disappeared: Pt. II
6×10 The Lost One
6×11 Voices
6×12 Destiny
6×13 Sacrifice

Story Reel: Death on Utapau
Story Reel: In Search of the Crystal
Story Reel: Crystal Crisis
Story Reel: The Bing Bang

Story Reel: The Bad Batch
Story Reel: A Distant Echo
Story Reel: On the Wings of Keeradaks
Story Reel: Unfinished Business

Dark Disciple Novel (Part I)
Lethal Alliance
The Mission
Dark Disciple

Son of Dathomir Comics
The Enemy of My Enemy
A Tale of Two Apprentices
Proxy War
Showdown on Dathomir

Dark Disciple Novel (Part II)
Saving Vos Part I
Saving Vos Part II
The Path

Star Wars Episode III Revenge of The Sith

So enjoy your Star Wars The Clone Wars marathon !


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