Putting The Clone Wars episodes in continuity order.

[Lord Insanity]

Over the past 3 or 4 months I have re watched the first 4 seasons of Clone Wars. I wanted to watch them in continuity order and the first 3 seasons are all over the place. I found this spoiler containing website and used it as a starting guide. So after watching the episodes mostly in the right order I made some minor positional changes base on obvious before/after clues from what I was watching. Some of the arcs could be placed differently but when in doubt I went with original airdate order as much as possible. So here is the completed episode order for all of stardestroyer.net to enjoy.

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Star Wars Episode II Attack of the Clones

Tartakovsky Animated Series:
001 Clone Wars - ch01-20
002 Clone Wars - ch21-22a (End after Padme sees Anakin's new eye scar)

Christophsis:
003 The Clone Wars - s2e16 - Cat and Mouse
004 The Clone Wars - s1e16 - The Hidden Enemy
005 The Clone Wars Movie

Malevolence:
006 The Clone Wars - s1e02 - Rising Malevolence
007 The Clone Wars - s1e03 - Shadow of Malevolence
008 The Clone Wars - s1e04 - Destroy Malevolence

Droids:
009 The Clone Wars - s1e06 - Downfall of a Droid
010 The Clone Wars - s1e07 - Duel of the Droids

Ryloth/Toydaria: (After "Malevolence" and "Droids")
011 The Clone Wars - s3e03 - Supply Lines
012 The Clone Wars - s1e01 - Ambush
013 The Clone Wars - s1e19 - Storm Over Ryloth
014 The Clone Wars - s1e20 - Innocents of Ryloth
015 The Clone Wars - s1e21 - Liberty on Ryloth

Gunray Captured:
016 The Clone Wars - s1e08 - Bombad Jedi
017 The Clone Wars - s1e09 - Cloak of Darkness
018 The Clone Wars - s1e10 - Lair of Grievous

Domino Squad: (After "Ryloth/Toydaria" and "Gunray Captured")
019 The Clone Wars - s3e01 - Clone Cadets
020 The Clone Wars - s1e05 - Rookies
021 The Clone Wars - s3e02 - ARC Troopers

Pirate Ransom:
022 The Clone Wars - s1e11 - Dooku Captured
023 The Clone Wars - s1e12 - The Gungan General

Maridun:
024 The Clone Wars - s1e13 - Jedi Crash
025 The Clone Wars - s1e14 - Defenders of Peace

Pantora:
026 The Clone Wars - s1e15 - Trespass

Naboo:
027 The Clone Wars - s1e17 - Blue Shadow Virus
028 The Clone Wars - s1e18 - Mystery of a Thousand Moons

Cad Bane:
029 The Clone Wars - s2e01 - The Holocron Heist
030 The Clone Wars - s2e02 - Cargo of Doom
031 The Clone Wars - s2e03 - Children of the Force

Geonosis:
032 The Clone Wars - s2e04 - Senate Spy
033 The Clone Wars - s2e05 - Landing at Point Rain
034 The Clone Wars - s2e06 - Weapons Factory
035 The Clone Wars - s2e07 - Legacy of Terror
036 The Clone Wars - s2e08 - Brain Invaders

Mandalore:
037 The Clone Wars - s2e12 - The Mandalore Plot
038 The Clone Wars - s2e13 - Voyage of Temptation
039 The Clone Wars - s2e14 - Duchess of Mandalore

Bounty Hunters:
040 The Clone Wars - s2e17 - Bounty Hunters

Zillo Beast:
041 The Clone Wars - s2e18 - Zillo Beast
042 The Clone Wars - s2e19 - The Zillo Beast Strikes Back

Boba Fett:
043 The Clone Wars - s2e20 - Death Trap
044 The Clone Wars - s2e21 - R2-D2 Come Home
045 The Clone Wars - s2e22 - Lethal Trackdown

Papanoida: (Cameo character George Lucas played in Episode III)
046 The Clone Wars - s3e04 - Sphere of Influence

Mandalore/Ziro the Hutt:
047 The Clone Wars - s3e05 - Corruption
048 The Clone Wars - s3e06 - The Academy
049 The Clone Wars - s3e07 - Assassin
050 The Clone Wars - s3e08 - Evil Plans
051 The Clone Wars - s1e22 - Hostage Crisis
052 The Clone Wars - s3e09 - Hunt for Ziro

Hunting Grevious: (After "Mandalore/Ziro the Hutt")
053 The Clone Wars - s2e11 - Lightsaber Lost (1st)
054 The Clone Wars - s2e09 - Grievous Intrigue (2nd)
055 The Clone Wars - s2e10 - The Deserter (3rd)

Peace Overtures:
056 The Clone Wars - s3e10 - Heros on Both Sides
057 The Clone Wars - s3e11 - Pursuit of Peace
058 The Clone Wars - s2e15 - Sentate Murders

Nightsisters: (All episodes aired in order from here on.)
059 The Clone Wars - s3e12 - Nightsisters
060 The Clone Wars - s3e13 - Monster
061 The Clone Wars - s3e14 - Witches of the Mist

Mortis (The Chosen One):
062 The Clone Wars - s3e15 - Overlords
063 The Clone Wars - s3e16 - Altar of Mortis
064 The Clone Wars - s3e17 - Ghosts of Mortis

Raid of the Citadel:
065 The Clone Wars - s3e18 - The Citadel
066 The Clone Wars - s3e19 - Counterattack
067 The Clone Wars - s3e20 - Citadel Rescue

Ahsoka Lost:
068 The Clone Wars - s3e21 - Padawn Lost
069 The Clone Wars - s3e22 - Wookiee Hunt

070-091 The Clone Wars Season 4 (in airdate order)

092-111 The Clone Wars Season 5 (in airdate order)

112+ The Clone Wars (Any further episodes or movies)

Tartakovsky Animated Series: (assuming "The Clone Wars" doesn't overwrite)
999 Clone Wars - ch22b-25 (Begin after Padme sees Anakin's new eye scar)
(Leads directly into Star Wars Episode III)

Star Wars Episode III Revenge of the Sith

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I minor controversy I found on the timeline website is a debate over what order the "Cad Bane" and "Mandalore/Ziro the Hutt" arcs should be. Spoiler

In the "Cad Bane" arc Cad Bane's droid Todo is destroyed. In the "Mandalore/Ziro the Hutt" arc Todo is mysteriously back. However in the first arc the characters clearly do not know each other while in the second one they do. Cad Bane getting a new mass produced consumer good (a droid) and simply uploading the old droids memory (which he could have copied before that mission) makes the most sense. Otherwise we would have to explain why the characters go from referring to each other by name to not knowing one another. There are also some other minor story and continuity points the make other arcs after "Cad Bane" but before "Mandalore/Ziro the Hutt"

[Jedipilot24]

The Clone Wars novel 'Wild Space' establishes that Anakin is receiving command of his first battle group and overlaps with the Droids arc; therefore they have to precede Malevolence. Otherwise it looks pretty good.
As for the other Clone Wars Novels, 'No Prisoners' occurs sometime before Maridun while the Gambit duology 'Stealth' and Siege' occur sometime after Maridun.

[Lord Insanity]

The intro montage from "Droids" makes reference to the "Malevolence" arc which places it after. I guess it is just a question of which you prefer to ignore, the specific time referenced in the novel or the montage in the episode. As I am completely ignoring anything but the movies and TV shows, I went with "Droids" after "Malevolence".

[Jedipilot24]

The intro montage from "Droids" makes reference to the "Malevolence" arc which places it after. I guess it is just a question of which you prefer to ignore, the specific time referenced in the novel or the montage in the episode. As I am completely ignoring anything but the movies and TV shows, I went with "Droids" after "Malevolence".

I just rewatched the intro montages to both 'Downfall of a Droid' and 'Rising Malevolence'. The former mentions, without showing, 'a series of defeats at the hands of General Grievous' which could, but need not, refer to the Malevolence trilogy. The latter, however, actually shows scenes from 'Downfall of a Droid'.
Take that however you prefer.

[Lord Insanity]

I just rewatched the intro montages to both 'Downfall of a Droid' and 'Rising Malevolence'. The former mentions, without showing, 'a series of defeats at the hands of General Grievous' which could, but need not, refer to the Malevolence trilogy. The latter, however, actually shows scenes from 'Downfall of a Droid'.
Take that however you prefer.

The opening montage to "Downfall of a Droid" does show space battle footage from "Rising Malevolence". If "Rising Malevolence" shows footage from "Downfall of a Droid" that just makes a mess doesn't it. The story seems to flow better with the Malevolence arc first from my viewing. If the one novel states the Droid arc is first and the opening montages are contradictory might as well go with that if you prefer then. Thanks for the input.

[AMX]

Domino Squad: (After "Ryloth/Toydaria" and "Gunray Captured")
019 The Clone Wars - s3e01 - Clone Cadets
020 The Clone Wars - s1e05 - Rookies
021 The Clone Wars - s3e02 - ARC Troopers

While these episodes do form a trilogy, they can not follow each other directly.

You may also want to check Leeland Chee's "Chronicling the Clone Wars" on the official Star Wars blog.

[Lord Insanity]

Domino Squad: (After "Ryloth/Toydaria" and "Gunray Captured")
019 The Clone Wars - s3e01 - Clone Cadets
020 The Clone Wars - s1e05 - Rookies
021 The Clone Wars - s3e02 - ARC Troopers

While these episodes do form a trilogy, they can not follow each other directly.

You may also want to check Leeland Chee's "Chronicling the Clone Wars" on the official Star Wars blog.

While "Rookies" could take place anytime after "Clone Cadets", "ARC Troopers" clearly comes right after "Rookies". Spoiler

The whole plot of "Rookies" is Grevious trying to get to Kamino without being detected by the listening post. "ARC Troopers" shows the Republic reinforcements showing up expecting Grevious and dealing with his attack. Grevious knew his attack was expected and performed diversionary tactics in an attempt to achieve his goal.

Looking through Chee's blog I have to wonder if he even watched the show. "Storm over Ryloth" obviously directly follows "Supply Lines" and "Ambush". Several story arcs running simultaneously might have been plausible if Obi-wan, Anakin, and Ashoka weren't in most episodes. Trying to do that with them ping-ponging from multiple areas at the same time is just stupid.