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.'