I don't like chronological rereads, I like thematic ones. But it's clear that my comic reading is taking me into the Clone Wars, and I'll probably use the opportunity to pick up some of the "missing 42" set in this time period, too. So a bit of housekeeping is in order.
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Between May 2002 and May 2005, there was a unified attempt to chronicle the events of the Clone Wars through adult novels, comics, short stories, YA books, video games and a cartoon series. These days this is referred to as the "Clone Wars Multimedia Project", although nobody called it that back in the day.
Remarkably, this project managed to tell a remarkably consistent and coherent story, largely due to each of the mediums staying well out of each other's way. We got a handful of good books (and a couple of stinkers) and some of the best Star Wars storytelling of all time in the comics. Tim Zahn wrote a short story about the Spaarti cloning cylinders. It was good times.
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In August 2008, Star Wars: The Clone Wars was released in cinemas. It was followed by six? seven? series of cartoons, ostensibly in the EU canon. It was clear from the start that The Clone Wars was not going to play nicely with the established canon, and by the end of the second series it was gleefully tearing up all sorts of established facts (most notoriously the Mandalorian continuity established by Karen Traviss). The days The Clone Wars is very highly regarded, mostly by people who were eight when it released. I watched the first series and, let's be honest with ourselves, it's not very good.
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It's become fashionable to head-canon The Clone Wars out of the EU continuity, and while tempting, this is a) the coward's way out; b) some elements from TCW become important in the EU: the Mortis arc is important in Fate of the Jedi and there's a (suprisingly deece) book where Ahsoka meets Callista and Gilad Pellaeon.
However, in the dying days of the EU there was no real attempt made to reconcile things, beyond the ridiculous idea that the entirety of the Clone Wars Multimedia Project took place within the first six months of the war.
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These days, my view on continuity is best captured by Chris Cerasi's famous "foggy windows" analogy:
"The analogy is that every piece of published Star Wars fiction is a window into the 'real' Star Wars
universe. Some windows are a bit foggier than others. Some are
decidedly abstract. But each contains a nugget of truth to them."
This is clearly the right way to deal with a whole number of contradictions and sticky continuity corners, and prevents us from having to accept stupid retcons like "Anakin killed a clone of Count Dooku ten months after Geonosis" (thanks, erm, The New Droid Army for Gameboy Advance).
I like to think that it's up to us, as individual readers, to decide which windows are clearer and which are foggier. I probably have what might be described as a "hipster" take on this. You can see where I'm going with this vis-a-vis TCW.
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Here's what I hold to be true: at some point towards the middle of the war, probably shortly after Jabiim, Anakin was assigned a junior padawan, Ahsoka, in the sort of way that a promising junior member of staff might manage a graduate trainee during one of their placements. Anakin, Ahsoka and Obi-Wan discharged a number of missions together. By the time the Outer Rim Sieges began, Ahsoka was long off the scene. Ryloth is a a tidal locked planet. Mandalore is as described in Karen Traviss' books. Bariss Offee serves at Drongar and later dies at Felucia, without bombing the Jedi temple. Darth Maul most certainly remains dead. Everything else takes place behind a thick, grimy, pub window.
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Here's what I'll engage with during my thematic saunter through the Clone Wars: the Mortis arc, because it's meant to be interesting and important to other EU works. The notorious Mandalorian arc, because I'm intrigued and because I hear some of the Obi-Wan character stuff gets referenced elsewhere. The Zillo Beast episodes because they sound fun and silly. POSSIBLY the Dathomir arc, out of a masochistic instinct to see how it's handled. POSSIBLY the Umbara arc, because it's meant to be great.