Star Wars' Clone Wars are an iconic and beloved part of the franchise, but fans have long questioned the conflict's name. While many battles take place within it, logic dictates that they're all part of a single, larger Clone War. However, one Star Wars Legends story justifies the plural 'Wars,' as well as closing a plot hole that existed in the original Expanded Universe (now the Legends canon.)
In Timothy Zahn’s Thrawn Trilogy, the original idea of the Clone Wars positioned the clones as enemies of the Jedi and the Republic. While this was eventually, technically true when the Clones were brainwashed into murdering the Jedi, the Thrawn Trilogy's account still seemed to disagree with the prequel trilogy's depiction of the war. Thankfully, the four-issue 'Siege of Saleucami' story arc of Star Wars: Republic (by John Ostrander and Jan Duursema) shows there's a clear explanation - one that also justifies the plural 'Clone Wars.'
Star Wars' CIS Had Its Own Clone Army
'Siege of Saleucami' makes it clear that the CIS created a Clone Army of its own, since most of its droids hardly posed a threat to Republic Clone Troopers and Jedi without overwhelming numbers. These Separatist clones fought the Republic on Saleucami in a miniature Clone War within the larger Clone Wars. But where did the CIS clones come from?
The Morgukai are an ancient Nikto death cult whose warriors are among the deadliest non-Force sensitives in the galaxy. The cult joined the CIS during the Clone Wars and their leader, Bok, allowed himself to be cloned, granting the Separatists their own clone warriors to credibly threaten the Republic’s finest Jedi and Clone Troopers. This Clone Army was known as the Morgukai Shadow Army and their collective homeworld, Saleucami, was the setting of a massive siege towards the end of the Clone Wars. While numerous Jedi and Clone Troopers fell during the battle, they proved superior to the Shadow Army and destroyed their cloning facility in a major Republic victory. This planet-spanning war was itself a 'Clone War,' and indeed introduces a whole other group of clones involved in the conflict.
Star Wars' Clone vs Clone Conflict Was a War Within a War
While the Clone Wars were largely fought between the Republic’s Jedi and Clone Troopers and the Separatists’ Sith and Battle Droids, the galaxy-spanning war included numerous smaller conflicts, including planetary battles fought between Republic loyalists and CIS militias, shifting the leadership of entire planets, and therefore justifying the Clone Wars' plural designation. The Siege of Saleucami was one such local Clone War, with the Jedi and the Republic’s Jango Fett clones battling the Separatists’ droids and Morgukai clones. The Thrawn Trilogy’s description of the Clone Wars may not coincide with the larger conflict seen in the Star Wars prequels, but it does describe one of these smaller Clone Wars.
The Siege of Saleucami is one of many instances of the Star Wars Legends era ensuring that every story counted, regardless of its medium. Timothy Zahn’s novels depicted an early concept of the Clone Wars, which was contradicted by the films but then reconciled by the Republic comics. In fact, the events of Republic’s 'Siege of Saleucami' arc are directly referenced in Star Wars: Episode III - Revenge of the Sith, which also includes its aftermath, in which Jedi Master Stass Allie is murdered upon Order 66’s execution. By tying multiple Star Wars Legends-era properties together, Republic ensured nothing was banished from the original canon, and showed fans why anyone involved in the Clone Wars wouldn't see it as one, singular conflict.