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In Attack of the Clones and Revenge of the Sith, the separatist organization is generally referred to as "the Separatists" and/or "the droid army". The pre-2008 Expanded Universe usually gave its full name as the "Confederacy of Independent Systems", sometimes shortened to "the Confederacy" or "the Separatists". Later, throughout The Clone Wars, it tends to get referred to as "the Separatist Alliance" and never (as far as I'm aware) the CIS, Confederacy, etc.

This seems like a fairly large change, since this is the name of the antagonist organization for a huge portion of the Star Wars series. "The Separatist Alliance" is apparently now the canon name, but as far as I know, it's never appeared before The Clone Wars and "the Confederacy" has rarely been used since--although it did make it into some other canon sources such as the Tarkin novel.

Is there any source for where these names came from and why they were changed? Out-of-universe/EU/canon sources are all fine.

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There are multiple explanations of the distinction between the Confederacy of Independent Systems and the Separatist Alliance. They may not all be entirely consistent.

The two terms are somewhat interchangeable

The Databank article suggests that the terms are interchangeable.

The Confederacy of Independent Systems, also known as the Separatist Alliance, was a collection of star systems and corporate titans that left the Republic and fought for independence against the Republic’s clone armies and Jedi Knights. The charismatic former Jedi Count Dooku was the Alliance’s political leader, while its military power came from credits and assets donated by powerful galactic trade groups.

There’s also a hint here that the Alliance might refer to the broader collection of CIS plus Trade Federation, etc. In any case, the terms CIS and Separatist Alliance were used both by Separatists and Republic allies, both in the early and later days of the war.

The Alliance predated the CIS

It seems that the Separatist Alliance may have come before the CIS, the former having "congealed" into the latter.

In the blink of an eye, it seemed, the galaxy was embroiled in a full-scale galactic war. The Separatist Alliance congealed into the Confederacy of Independent Systems, a coalition of loosely aligned worlds united for war.

Star Wars Propaganda: A History of Persuasive Art in the Galaxy

The most likely conclusion from this would be that the Separatist Alliance didn’t take on the name “CIS” until there were enough planets and systems involved for there to be a proper government. Dooku’s early efforts were primarily bankrolled by trade and financial groups. There might also be an implication of increasing formalization.

Nor would this be the first name change that the Alliance underwent. This early poster refers to Dooku as the head of “the Independent Movement for Self-Determination.”

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Some of it is propaganda

Each side chooses the terminology that makes itself look good, while trying to label the other side as something negative. One person’s rebel is another person’s terrorist.

“Confederacy of Independent Systems” or “CIS” seems to the be the CIS’s own formal and preferred term for itself. All the CIS propaganda in Star Wars Propaganda: A History of Persuasive Art in the Galaxy refers to the Confederacy of Independent Systems, not the Separatist Alliance.

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By contrast, officials of the Republic, as well as people not politically affiliated with the Separatist cause, tend to use the term “Separatist.” This is what the pro-Republic artist Janyor of Bith calls it:

I have been a propagandist, a young defender of the Republic, blind to its faults and gripped by a jingoist’s fervor to support the soldiers of the Clone Wars. I believed in the rhetoric of Chancellor Palpatine. I believed in the evils of Count Dooku and the selfish damage inflicted by the Separatist Alliance.

Star Wars Propaganda: A History of Persuasive Art in the Galaxy

This is also occasionally illustrated in the Clone Wars series:

AHSOKA: Who’s he?

PADME: He is a she, a senator in the Confederacy Of independent systems.

AHSOKA: Your friend is a separatist? One of Dooku’s pawns?

PADME: The separatists used to be a part of the Republic.

The Clone Wars, “Heroes on Both Sides”

The phrase “Confederacy of Independent Systems” seems designed to convey an air of legitimacy, and thus tends to be preferred by the CIS itself. By contrast, “Separatist” is a more neutral or even derogatory term (“the Separatists”).

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  • Interesting! I didn't know about the propaganda book. Re: the third option, it seems like the Separatist characters in TCW say it fairly often as well--e.g. a battle droid says something like "answer for your crimes to the Separatist Alliance" in S5 A War on Two Fronts.
    – Milo P
    Dec 14, 2016 at 17:45
  • I'd love to sit in on a lecture given by Dooku Dec 14, 2016 at 19:31
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The 'Confederacy of Independent Systems' became known as the 'Separatist Alliance' during the time of 2008 The Clone Wars television show. This was so they could avoid using the word 'Confederacy' in a children's show and prevent busybody parents from submitting complaints despite the fact that it's simply a form of government and the term is not solely in reference to the Confederate States of America (as some Americans believe it to be). It is simply real-world censorship with no legitimate in-universe explanation.

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    That makes sense, especially given Disney's touchiness on the subject (was it Disney back then). Could you find a reference for this? Jun 9, 2017 at 13:19
  • It would be interesting also to know if the CSI is called CSI intead of Separatist Alliance in any Disney canon material.
    – Neow
    Jun 9, 2017 at 13:45
  • Disney acquired Lucas properties in 2012 - so, well before Disney became involved
    – NKCampbell
    Jun 9, 2017 at 13:47
  • @Neow In a couple of sources--Adamant's answer mentions an episode of TCW that uses it, and it's also in Tarkin. Not sure about the canon status of the propaganda book, but I'd guess it's canon too.
    – Milo P
    Jun 9, 2017 at 15:11
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    @MiloP Thanks! Everything published after Disney bought Lucasfilm is considered canon. The propaganda book (written by Pablo Hidalgo btw) is certainly canon.
    – Neow
    Jun 10, 2017 at 18:44

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