In my personal SW Universe, there are three different clone wars. Only the Third Clone War makes an appearance in my PT, though, as the first two occur decades before the events in my rewrite.
Here's a rundown of all three Clone Wars:
First Clone War (78-75 BBY)
Prior to the First Clone War -- or the New Mandalorian War as it was known as at the time -- the Mandalorian civilization had been at peace with the Old Republic for thousands of years. This all changed, however, when Ranah Teh Naast -- an insane clone -- rose to power over the Mandalorians and crowned herself Mandalore the Destroyer.
A incredibly charismatic ruler, Mandalore the Destroyer managed to convince most of her people that they had grown complacent and stagnant in the millennia following the original Mandalorian Wars, that they were allowing their culture to die out through slow assimilation into the Republic. So, with these fears in their minds and hearts, the Mandalorians allowed themselves to be thrown into a war against the Republic.
Having grown complacent themselves over the millennia, the Republic didn't have a large standing military and they found themselves unable to adequately defend themselves when the Mandalorians invaded, leaving only the Jedi -- who did have a massive army -- to defend them.
At first, the Mandalorians were victorious; not only was their army twice the size of the Jedi's, but they had managed to nearly cripple the Jedi army by capturing and destroying many key shipyards and military installations. However, Mandalore's own unstable mind proved to be her own undoing, and she began making decisions which led to more-and-more losses to the Republic.
In the end, the Mandalorians found themselves facing destruction at the hands of the Republic, but Mandalore -- conceited and insane -- refused to make peace. Finally fed up, a faction of Mandalorian dissidents assembled and staged a coup, assassinating the insane clone and ending the war in the process.
There was to be no peace for the Mandalorians, however. With Mandalore the Destroyer gone, a power vacuum was left behind, and the Mandalorians -- those who had rebelled against her and those who had remained faithful -- became embroiled in a civil war. Eventually, this civil war led to the devastation of their capital world and the fall of their civilization.
Second Clone War (63-54 BBY)
In the years following the end of the First Clone War, many systems became dissatisfied and disenchanted with the Republic for failing to protect them and their interests during the war and began calling for reform within the Senate. The Senate refused to listen to their pleas, however, and basically ignored them.
When the Count Doku of Serreno, a former Jedi master who had left the Coruscanti Order after becoming disillusioned with their principles, came out of seclusion and became their spokesman, these disenchanted systems assembled together into a unified secessionist movement known as the Confederacy of Independant systems and began crying for separation from the Republic. Their demands were made peacefully, diplomatically, but the Senate refused to offer any concessions or make any compromises, leading to increased tensions between the two sides.
Finally, it all came to a head when a group of Republican spies were captured and imprisoned on the Separatist world of Geonosis. Instead of operating through proper channels, the Republic sent a squad of Jedi in to forcibly extract the prisoners from captivity, sparking off a large battle between Separatist and Republican forces.
In the wake of the Battle of Geonosis, the Confederacy of Independant Systems ended all talks with the Republic and declared its worlds officially free of Republican governance. In reply, the Republic declared war against the Separtists.
Following the First Clone War, neither the Republic nor the Confederacy had populations large enough to support large armies. The Separatists, however, had managed to overcome this handicap by creating a large army made up of formidible battle 'droids. The Republic, in turn, contracted Spaarti Creations -- a large biotech firm which specialized in cloning -- to grow a clone army to use against the Separatists. Using top-of-the-line cloning techniques, Spaarti Creations cloned the first clone shock troopers within a year's time on their headquarters world of Cartao, and the war began in earnest.
The war was long and bloody, and many Jedi, feeling that the Separatists were in the right, left the Republic to side with the Confederacy. As the war raged, both sides became increasingly corrupt and committed countless atrocities. More-and-more politicians with loyalties to the military were elected into the Senate, leading the Republican government to become ever more militant.
The Second Clone War finally came to an end with the Battle of Coruscant and the Mission to Mustafar. Doku was slain aboard his flagship the Invisible Hand, decapitated in a duel against his own son, Jard, while the other leaders of the Confederacy were all slaughtered while in hiding on the world of Mustafar by Dark Jedi assassins under orders from the Republic. With the head of the Confederacy cut off, it soon fell apart, leaving the Republic victorious.
In the wake of the defeat of Doku and the Separatists, the Galactic Republic was reformed into the Galactic Empire. Cos Dashit -- an admiral who had won many major victories for the Republic -- was crowned emperor, and the Senate -- which had originally been headed by a democratically-elected president -- was now headed by a supreme chancellor, the emperor's personally-appointed representative.
Third Clone War (53-35 BBY)
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 hierarchal ladder until he succeeded in becoming the president of Spaarti Creations.
Once in power, he began using the resources at his command to begin the realization of his dream -- to create a perfect civilization built on the foundations of eugenics and genetic engineering. As the atha prime, he personally supervised the creation of a new batch of clones -- clones who were genetically modified to be wholly subserviant to him and his fellow athas. Using these clones, he secretly deposed and replaced important figures in the Cartao goverment with replicas who answered to him. In a few short months, he became the silent ruler of the entire planet.
With Cartao now under his control, he began to plan ahead, to spread his power to other worlds. All subsequent shock troopers produced for the Republic were engineered for complete subserviance, 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 clone shock troopers 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 formidible warships.
Thus began the Third Clone War. The clones became figures of terror as they conquered worlds upon worlds, harvesting billions for their genetic material. Jedi and other Force-sensitives became specific targets of the Clonemasters, as their DNA was used to grow Force-sensitive generals for their armies.
The Imperials, left largely with a fleet of older model Venator-class star defenders, struggled to fight back against the Clonemasters 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 Clonemasters were rounded up and taken into Imperial captivity.
With the end of the Third Clone War, the athas where all tried and convicted of war crimes and sentenced to life imprisonment while the Senate passed a series of laws which made cloning completely illegal.
The Clone Wars proved to be the Known Regions' bloodiest conflict, with more than a 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 36,000,000,000. 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.