Second Clone War (Divergent Universe)

"We do not recognize the Separatists. They are an illegitimate body, little removed from rebels or terrorists. If we were to kowtow to their demands, to allow secession, this war-weakened Republic -- which has stood for a thousand generations -- would surely collapse. And make no mistake; they, too, would collapse with us, as they would be no more capable of self-sufficiency following such division than we would. No, we will not allow separation. Any system, any world, that attempts such action will be met with swift, sure, fierce resistance."

- President Finis Valorum, in a public statement made a year prior to the Battle of Geonosis

The Second Clone War, originally known as the Clone War, was a fullscale war fought between the Galactic Republic and the Confederacy of Independent Systems.

Prelude
In the years following the end of the First Clone War, many systems became dissatisfied and disenchanted with the Republic for having failed 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 Count Tyran Dohku of Serreno, a former Jedi master who had left the Order of Coruscant 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 Independent systems and began calling 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 Republic forces.

In the wake of the Battle of Geonosis, the Confederacy of Independent Systems ended all talks with the Republic and declared its worlds officially free of Republican governance. In reply, the Republic declared war against the Separatists.

The event
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 formidable 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 shocktroopers within a year's time in their headquarters on Cartao and the war began in earnest.

The war was long and bloody. 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. Dohku was slain aboard his flagship the Invisible Hand, beheaded 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 evil Jedi assassins under orders from the Republic. With the head of the Confederacy cut off, it soon fell apart, leaving the Republic victorious.

Aftermath
In the wake of the defeat of Count Dohku 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 during the First Clone War and the first fourth of the Second -- 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.