The secession of so many star systems is unprecedented; there hasn't been a crisis like this in the history of the Republic.
The Confederacy of Independent Systems Crisis (9—11 ArS), also known as the CIS Crisis, the Separatist Crisis, and the Secession Crisis, was the term given to the period of tension that immediately preceded the Clone Wars, which this crisis ushered in.
Even through there was tension before the crisis, it truly began when the former Jedi Master, Count Maxon Dooku, appeared on Raxus Prime and declared his intentions of forming a Separatist movement, claiming that the Galactic Republic was failing in its duties to serve those whom it presided over.
Supreme Chancellor Palpatine's eight-year term in office expired in 11 ArS, but the Republic's Senate amended the Constitution so that Palpatine could remain in office indefinitely. The law also gave the Chancellor all authority to attempt to put an end to the Crisis, including declaring martial law on local systems.
Meanwhile, negotiations between the Republic and the Separatists were thwarted by repeated terrorist bombings, which were carried out by assassins hired by Dooku, under orders from Darth Sidious, Dooku's master, who was the true leader of the Separatists.
The uneasy peace between the two governments eventually fell through, thanks to an incident on the planet of Geonosis, in which Jedi Knight Obi-Wan Kenobi was captured on-planet, and charged with espionage, earning him a death sentence. Later, Kenobi's Padawan, Anakin Skywalker, and Senator Padmé Naberrie of Naboo attempted to rescue Kenobi, but they themselves were also captured, and sentenced to die with Kenobi in the Petranaki arena, but were rescued, by the combined efforts of Mace Windu's Jedi strike team, and the timely arrival of Jedi Master Yoda with an army comprised of clones—one that had been in the process of being created, without the knowledge of the Jedi or Republic, for over ten years.
The Republic emerged victorious against the Separatist Droid Army on Geonosis, but Count Dooku's escape allowed the Clone Wars to begin, which was just exactly what Dooku's Sith Master, Sidious, the surreptitious instigator of the war, wanted.
Soon, the next stage of the grand plan shall be put into motion.
—Darth Sidious, to Count Maxon Dooku
Ever since becoming the Dark Lord of the Sith, Darth Sidious had concocted a plan to annihilate the Jedi, the ancient enemies of the Sith, and dismantle the Galactic Republic, transforming it an empire, with himself as Emperor.
As his alter ego, Palpatine, Sidious manipulated the Republic's failing bureaucracy, orchestrating his ascension from the Senator of Naboo, to Supreme Chancellor of the Republic; the first step of his master plan was complete. However, Sidious had lost his first apprentice; a new one was required in order to put the next phase of his scheme into effect.
Dooku's disillusionment with the Galactic Senate and the Jedi was no secret to Sidious; Dooku was likely under Palpatine's influence even before his fall. However, Dooku had not yet become a Sith, nor was he aware that Palpatine's secret identity was Darth Sidious. After the Invasion of Naboo, which resulted in the death of his former apprentice, Qui-Gon Jinn, Dooku became even more apprehensive towards the Jedi, but still gave some thought to hunting down the hidden second Sith. However, he concluded that even eliminating the Sith Master would not halt what he felt was the inevitable advance of the dark side. Shortly thereafter, Dooku was approached directly by Sidious, and they had a long conversation, in which Dooku, found that Palpatine's own objectives, were not that different from his own.
Despite the recent death of Jinn at the hands of Darth Maul, Sidious' first apprentice, the dark lord found it surprisingly easy to convince Dooku to ally with the Sith; after seventy years in the Jedi Order, Dooku abandoned his former allies, along with the Jedi way, and embraced the dark side of the force.
Dubbing his new apprentice Darth Tyranus, Sidious instructed him to go to the planet of Kamino, where Dooku's old friend, Master Sifo-Dyas, had ordered the creation of a clone army. Tyranus completed his mission, slaying his old comrade, and paid for the army's creation.
With the creation of the army is progress, Tyranus erased the Jedi archives information on Kamino, as well as other planets and star systems. The ex-Jedi also stole secret Jedi hyperspace routes through the center of the galaxy, knowing it could be put to use in the coming years.
From Dooku's fall in 3 ArS, until the beginning of the crisis, Sidious developed his plan, adapting it as the situation changed over the six years of his Chancellorship, including a re-election in 7 ArS.
When the year 9 ArS came around, all the pieces on Sidious' game-board were in place; thus, he began to move the pieces, preparing to spark the conflict, that would, according to his plans, see the end of both the Republic, and the Jedi.