The Clone Wars Story Arcs

This list is ordered chronologically as found in this article

⇒ Christophsis
┌ S2E16: Cat and Mouse
└ S1E16: The Hidden Enemy

The Hutts: The Clone Wars (2008)

Kamino¹: S3E01: Clone Cadets

Ryloth: S3E03: Supply Lines

Toydaria: S1E01: Ambush

⇒ Malevolence
┌ S1E02: Rising Malevolence
├ S1E03: Shadow of Malevolence
└ S1E04: Destroy Malevolence

Kamino¹: S1E05: Rookies

⇒ Astromech Rivalry
┌ S1E06: Downfall of a Droid
└ S1E07: Duel of the Droids

Troublesome Gunray
┌ S1E08: Bombad Jedi
├ S1E09: Cloak of Darkness
└ S1E10: Lair of Grievous

⇒ Pirates on Florrum
┌ S1E11: Dooku Captured
└ S1E12: The Gungan General

⇒ Lost on Maridun
┌ S1E13: Jedi Crash
└ S1S14: Defenders of Peace

Pantora: S1E15: Trespass

⇒ Danger on Naboo
┌ S1E17: Blue Shadow Virus
└ S1E18: Mystery of a Thousand Moons

⇒ Ryloth
┌ S1E19: Storm Over Ryloth
├ S1E20: Innocents of Ryloth
└ S1E21: Liberty on Ryloth

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⇒ Cad Bane
┌ S2E01: Holocron Heist
├ S2E02: Cargo of Doom
└ S2E03: Children of the Force

Pirates on Felucia: S2E17: Bounty Hunters

⇒ Zillo Beast
┌ S2E18: The Zillo Beast
└ S2E19: The Zillo Beast Strikes Back

⇒ Rush Clovis
┌ S2E04: Senate Spy
└ S2E05: Landing at Point Rain

⇒ Geonosis
┌ S2E06: Weapons Factory
├ S2E07: Legacy of Terror
└ S2E08: Brain Invaders

⇒ Grievous
┌ S2E09: Grievous Intrigue
└ S2E10: The Deserter

Lightsaber Lost: S2E11

⇒ Mandalore
┌ S2E12: The Mandalore Plot
├ S2E13: Voyage of Temptation
└ S2E14: Duchess of Mandalore

⇒ Boba Fett
┌ S2E20: Death Trap
├ S2E21: R2 Come Home
└ S2E22: Lethal Trackdown

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⇒ Mandalore
┌ S3E05: The Mandalore Plot
└ S3E06: Voyage of Temptation

Kamino¹: S3E02: ARC Troopers

Pantora: S3E04: Sphere of Influence

⇒ Ziro the Hutt
┌ S3E08: Evil Plans
├ S1E22: Hostage Crisis
└ S3E09: Hunt for Ziro

⇒ Politics
┌ S3E10: Heroes on Both Sides
├ S3E11: Pursuit of Peace
└ S2E15: Senate Murders

⇒ Dathomir
┌ S3E12: Nightsisters
├ S3E13: Monster
└ S2E14: Witches of the Mist

⇒ Mortis
┌ S3E15: Overlords
├ S3E16: Altar of Mortis
└ S2E17: Ghosts of Mortis

⇒ Citadel
┌ S3E18: Citadel
├ S3E19: Counter Attack
└ S2E20: Citadel Rescue

⇒ Lost on Felucia
┌ S3E21: Padawan Lost
└ S3E22: Wookiee Hunt

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⇒ Mon Cala
┌ S4E01: Water War
├ S4E02: Gungan Attack
└ S4E03: Prisoners

Naboo: S4E04: Shadow Warrior

⇒ Droids Lost
┌ S4E05: Mercy Mission
└ S4E06: Nomad Droids

⇒ Umbara
┌ S4E07: Darkness on Umbara
├ S4E08: The General
├ S4E09: Plan of Dissent
└ S4E10: Carnage of Krell

Zygerria
┌ S4E11: Kidnapped
├ S4E12: Slaves of the Republic
└ S4E13: Escape from Kadavo

Mandalore: S4E14: A Friend in Need

⇒ Rako Hardeen
┌ S4E15: Deception
├ S4E16: Friends and Enemies
└ S4E17: The Box

Crisis on Naboo: S4E18

⇒ Betrayed Assassin
┌ S4E19: Massacre
└ S4E20: Bounty

⇒ Darth Maul
┌ S4E21: Brothers
└ S4E22: Revenge

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⇒ Onderon
┌ S5E02: A War on Two Fronts
├ S5E03: Front Runners
├ S5E04: The Soft War
└ S5E05: Tipping Points

⇒ Youngling Adventure
┌ S5E06: The Gathering
├ S5E07: A Test of Strength
├ S5E08: Bound for Rescue
└ S5E09: A Necessary Bond

⇒ D-Squad
┌ S5E10: Secret Weapons
├ S5E11: A Sunny Day in the Void
├ S5E12: Missing in Action
└ S5E13: Point of No Return

⇒ Brothers on Mandalore
┌ S5E01: Revival
├ S5E14: Eminence
├ S5E15: Shades of Reason
└ S5E16: The Lawless

⇒ Ahsoka
┌ S5E17: Sabotage
├ S5E18: The Jedi Who Knew Too Much
├ S5E19: To Catch a Jedi
└ S5E20: The Wrong Jedi

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⇒ Good Soldiers follow Orders
┌ S6E01: The Unknown
├ S6E02: Conspiracy
├ S6E03: Fugitive
└ S6E04: Orders

⇒ Clovis
┌ S6E05: An Old Friend
├ S6E06: The Rise of Clovis
└ S6E07: Crisis at the Heart

⇒ Jar Jar on Bardotta
┌ S6E08: The Disappeared, Part I
└ S6E09: The Disappeared, Part II

The Lost One: S6E10

⇒ Trials of the Force
┌ S6E11: Voices ├ S6E12: Destiny
└ S6E13: Sacrifice

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⇒ The Bad Batch
┌ S7E01: The Bad Batch
├ S7E02: A Distant Echo
├ S7E03: On the Wings of Keeradaks
└ S7E04: Unfinished Business

⇒ The Martez Sisters
┌ S7E05: Gone with a Trace
├ S7E06: Deal No Deal
├ S7E07: Dangerous Debt
└ S7E08: Together Again

⇒ The Finale
┌ S7E09: Old Friends Not Forgotten
├ S7E10: The Phantom Apprentice
├ S7E11: Shattered
└ S7E12: Victory and Death

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Star Wars Episode III: Revenge of the Sith
Season 7 of The Clone Wars happens concurrently to this Movie.
At the end of the movie, Season 1 Episode 1 of The Bad Batch: “Aftermath” also overlaps with the events.