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 was one such local Clone War, with the Jedi and the Republic’s Jango Fett clones battling the Separatists’ droids and Morgukai clones. 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. This planet-spanning war was itself a 'Clone War,' and indeed introduces a whole other group of clones involved in the conflict.

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 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. 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. The Morgukai are an ancient Nikto death cult whose warriors are among the deadliest non-Force sensitives in the galaxy. These Separatist clones fought the Republic on Saleucami in a miniature Clone War within the larger Clone Wars. '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.

Thrawn trilogy clone wars