Third Clone War (Divergent Universe)

"Long have I dreamed of a Galaxy purged of all genetic aberration and imperfection. With half the Imperial fleet now under my command, I can finally begin making that beautiful dream a beautiful reality."

- Atha Prime Iain Cadmus

The Third Clone War was a fullscale war fought between the Galactic Republic and the Athan Directorate.

Prelude
The seeds for the Third Clone War were planted and began to sprout while the Second Clone War was still being fought.

Iain Cadmus, the atha prime -- or head clonemaster -- of Spaarti Creations began accruing more and more power within the company, working his way up the hierarchical ladder until he succeeded in becoming the CEO of Spaarti Creations.

Once in power, he began using the resources at his command to begin the realization of his dream: the creation a perfect civilization built on the foundations of genetic engineering and eugenics. As the head of the Athan Directorate, he personally supervised the creation of a new batch of clones -- clones who were genetically modified to be wholly subservient to him and his fellow athas. Using these clones, he secretly deposed and replaced important figures in the Cartao government with replicas who answered to him. In a few short months, he became the silent ruler of the entire planet.

With Cartao now under the control of the Directorate, Cadmus began to plan ahead to spread his power to other worlds. All subsequent shocktroopers produced for the Republic were engineered for complete subservience, all with the full approval of the Senate, the members of which believed that unquestioning clones would make for better soldiers on the battlefield. Unbeknownst to them, Cadmus had also encoded these new clones with post-hypnotic suggestions which would cause them to rebel against their Republican commanders upon his order.

Months following the defeat of the Confederacy and the Republic's transformation into the Empire, Cadmus went through with his plan and issued Order 66 on a special frequency to all clone fleets throughout the Empire. Receiving this transmission, the shocktroopers turned against their Imperial masters, slaughtering them and taking full control of their ships. Within hours, Iain Cadmus -- the atha prime of Spaarti Creations -- had control over an entire vast fleet of formidable warships.

The event
The clones became figures of terror as they conquered worlds upon worlds. The eugenics program of the Directorate was imposed upon these captured populaces, leading to the extermination of billions of lives deemed "genetically impure" by Athan standards. Conversely, those considered "genetically paramount" were rounded up and harvested for their genetic material; Jedi and other Force-sensitives became specific targets of the Clonemasters, as their DNA was used to grow Force-adept commanders for their armies.

The Imperials, left largely with a fleet of older model Venator-class star defenders, struggled to fight back against the Directorate with their newer Imperator-class star destroyers. They managed to hold their own against the clones, however, and slowly but surely, the Imperials began to recover from the initial clone assaults and reacquire captured planets and resources.

The Third Clone War was the longest and bloodiest of all the Clone Wars. It finally came to an end when Cartao itself was invaded and captured and all the Directorate members were rounded up and taken into Imperial custody.

Aftermath
With the end of the Third Clone War, the athas were all tried and convicted of war crimes and sentenced to life imprisonment while the Senate passed a series of laws making the cloning of sapient beings completely illegal.

Together, the three Clone Wars proved to be the Known Regions' bloodiest conflict, with more than six-trillion beings losing their lives. The various sects of Jedi, who had started out so great in number that together they had had their own standing army, were reduced down to a mere 36 billion. Entire worlds were left depopulated.

The economy, too, was devastated, leading the Empire into a severe depression. With this depression, corruption began to sweep through the Senate. Son Hhat, the second emperor, proved to be a far weaker leader than his predecessor and became a puppet of the corrupt senators. This all eventually paved the way for Palpatine's rise to power.