Sidious spent decades planning to destroy the Jedi and dismantle the Republic… the Clone Wars were the culmination of those efforts.
The Clone Wars (11—16 ArS), also known as the Clone War, the Great Clone War, the Clone-Droid War, and less commonly known as the War of Secession, the Separatist-Republic War, and Darth Sidious' War, was the name given to the major galactic conflict that featured the Galactic Republic and the Jedi Order fighting against a strong secessionist movement—the Confederacy of Independent Systems.
The war was named after the clone troopers utilized by the Republic, who battled the battle droid forces of the CIS. These armies, the Grand Army of the Republic and the Separatist Droid Army, were two of the largest ever pitted against each other in galactic history, since each side possessed massive amounts of their own types of soldiers.
The fighting between them rapidly spread to countless populated worlds, and starting with the Battle of Geonosis, both sides scored major victories over the other, and at different periods of the war, either seemed likely to achieve victory. As a result of the conflict, numerous worlds were laid to ruin in the war's numerous battles.
However, in 16 ArS, the death of Count Maxon Dooku, the Separatist Head of State, during the Battle of Coruscant, and that of General Grievous, the leader of the droid armies, during the Battle of Utapau, coupled with the deactivation of the droid army, brought about an end to the fighting. The Treaty of Corellia—signed the same day as the Mission to Mustafar—officially ended the war. At the time, it was the largest galactic war to date.
Unknown to most of those involved, the conflict was set in motion, and, for the five years of its duration, preserved, by the Dark Lord of the Sith, Darth Sidious, whose ultimate goal was the transformation of the Republic into an Empire with himself as Emperor; also, as a Sith Master, Sidious' sought the complete eradication of the Jedi Order, the Sith's ancient enemies.
Despite controlling the Republic as Supreme Chancellor Palpatine, and the Separatists through Dooku, who was his secret apprentice, Sidious' plans were ultimately thwarted, and he was forced to flee known space.
I will not let this great Republic—which has stood for over twenty-five thousand years—be split in two; my negotiations will not fail."
"But if they do, you must realize there aren't enough Jedi to protect the entire Republic; we are keepers of the peace, not soldiers.
—Palpatine and Mace Windu
Crisis on Naboo and Palpatine's Rise
Although the Clone Wars officially began in 11 ArS at the Battle of Geonosis, it's beginning could be found eight years prior, during the invasion of the planet of Naboo by the Trade Federation, in response to Outer Rim trade route taxations imposed by the Galactic Senate. The aftermath saw the ascension of Naboo Senator Palpatine to the office of Supreme Chancellor of the Galactic Republic. He promised to bring an end to the corruption that had so often plagued the Republic's Senate.
However, the four years of his first term saw barely anything to fulfill that promise. The demilitarization of the Trade Federation was viewed by many as little more than a slap on the wrist, and Nute Gunray, Viceroy of the Trade Federation, managed to evade any serious charges against him, due to his role in the Naboo conflict, despite opposition from Padmé Naberrie, Queen of Naboo.
Moving the Pieces into Place
Can you do what must be done? Will you aid me in the restoration of the galaxy?"
"Then Maxon Dooku shall cease to exist; you are Darth Tyranus—Dark Lord of the Sith. Rise, my new apprentice.
—Darth Sidious and Count Maxon Dooku
During this time, Palpatine, through his true persona— that of the Sith Master Darth Sidious—contacted the former Jedi Master Maxon Dooku, now the Count of Serenno; this was because Darth Maul, Sidious' first apprentice, had been slain by Obi-Wan Kenobi during the final battle of the Naboo crisis. Now, Sidious was in need of a new apprentice—Dooku, an accomplished Jedi, who had long criticized the corruption in the Republic's Senate, and had blamed the Jedi High Council for turning a blind eye to the Senate's unscrupulousness, had just resigned from the Order; he held the Jedi Council responsible for the death of his former Padawan, Master Qui-Gon Jinn, at Maul's hands.
Taking advantage of Dooku's disillusionment, Sidious convinced the ex-Jedi that the galaxy needed to be reforged; the Republic needed to be destroyed, along with the Jedi, so that a new order could rise, free of the blood and carnage of the past. After seventy years in the Jedi Order, Dooku forsook the Jedi way, and embraced the dark side of the Force.
Apprenticing himself to Sidious, Dooku was renamed Darth Tyranus and became a Dark Lord of the Sith. With his family holdings on Serenno, Dooku possessed vast quantities of wealth that he used in the service of his new Master.
Just after Dooku left the Jedi, his old friend, Master Sifo-Dyas, secretly made an order from Kamino—a planet inhabited by a a race of cloners—for an army to be cloned for the Jedi and the Republic. Sidious learned of this, and informed Dooku, instructing him to eliminate his former friend and gain control over the army. Dooku obeyed, murdering the Jedi Master, then paying for Sifo-Dyas's clone army under his Sith name.
Later, Dooku returned to the Jedi Temple, in secret, to erase Kamino, and thirty-seven other star systems from the Jedi Archives, preventing the Jedi from discovering the clone army—an army being grown for them, without their knowledge—until the time was right for them to discover its existence. Dooku also stole information about secret Jedi hyperspace routes through the Deep Core region in the center of the galaxy.
Orchestrating a Crisis
In 9 ArS, Dooku appeared on Raxus Prime, announcing his intent to establish the Confederacy of Independent Systems, a group of organizations and governments whose goal was to secede from the Republic due to their common belief that they'd been cheated by the Republic and its corruption.
By 11 ArS, after many systems had left the Republic to join the Confederacy, the Senate, fearful of this growing Separatist movement, passed the Emergency Powers Act, an amendment to the Galactic Constitution that eliminated the two-term limits for the position of Chancellor, and allowed Palpatine to remain in office until the crisis had passed.
Dooku, though unable to openly take his own apprentice due to the Rule of Two, did seek out several Force-sensitives to serve him as Dark Acolytes. These beings included Asajj Ventress, Sev'rance Tann, Tol Skorr, Kadrian Sey, Artel Darc, Karoc, Vinoc, Saato, Trenox, and even, for a time, Jedi Master Quinlan Vos. All, with the exception of Vos, were killed during the war.
In addition to this group of Dark Jedi, he recruited the Chistori warrior Cydon Prax, as well as the Gen'Dai bounty hunter Durge, who, if for no other reason than to destroy the Republic's army of clone troopers bred from the DNA of Mandalorian Jango Fett—as Durge hated Mandalorians—joined the Confederacy.
The most important—and most notorious—of Dooku's allies was the Kaleesh warrior Qymaen jai Sheelal, whose body had been horribly maimed in a shuttle crash—one arranged, though not known to Sheelal, by Dooku himself. His broken body was taken to Geonosis where he was offered a new life and the help of the InterGalactic Banking Clan for his people by the its Chairman, San Hill. All the Kaleesh had to do, in exchange, was lead the Separatist Droid Army against the Republic who had wronged his people.
Ando, Geonosis, Tynna, Sy Myrth and Yag'Dhul were some of the first worlds to secede from the Republic. They would be joined by the Elrood, Danjar, Tantra and Sluis sectors, bringing most of the Rimward leg of the Rimma Trade Route under the control of the CIS. These sectors would be followed by the Abrion sector, which provided the Separatists with over two-hundred agricultural worlds, and the Lahara sector, which gave Agamar, Oorn Tchis and the Mirgoshir hyperspace crossroads to the Confederacy. Though Ando joined the CIS, the Andoan Free Colonies remained loyal to the Republic. Later, these sectors and planets would be joined by the corporate entities of the galaxy—the Baktoid Armor Workshop, the Commerce Guild, the Corporate Alliance, the Techno Union, the InterGalactic Banking Clan and the Trade Federation.
At this time, the Republic capital world of Coruscant found itself the target of many terrorist attacks, including an attack on Padmé Naberrie—the Senator of Naboo, who used the regnal name Amidala—ordered by Dooku and Nute Gunray, Trade Federation Viceroy, and carried out by Jango Fett and Zam Wesell, upon her return to vote on the Military Creation Act, which would give the Chancellor the authority to constitute an army to defend the Republic against the threat posed by Separatists.
After a second attack on Naberrie's life, the Jedi Council selected Obi-Wan Kenobi to investigate who was behind the attempted assassinations on the Senator, while his Padawan, Anakin Skywalker escorted Naberrie back to Naboo. Kenobi's search took him to Kamino, where he discovered the clone army, already with two hundred thousand units combat-ready, and a million more in production. He also encountered Jango Fett, who attempted to escape with his son to Geonosis, but was pursued by Kenobi, who managed to send a message to the Jedi Council, before being captured. On Tatooine, Skywalker was directed by Mace Windu to stay where he was, and protect Naberrie. However, Padmé decided to travel to Geonosis to rescue Kenobi, and Anakin came with her. However, they both were captured, as well, and, along with Kenobi, were, by order of Archduke Poggle the Lesser, a prominent Separatist leader, to be executed.
With the knowledge that a Confederate army was in production, the Senate, at behest of Representative Jar Jar Binks—who had been manipulated by Vice Chair Mas Amedda—gave Chancellor Palpatine emergency powers, effectively making him a dictator. With this newly-granted power, Palpatine legalized the creation of the clone army to serve in the Grand Army of the Republic.
The Battle of Genosis
I have good news for you, my lord—the war has begun."
"Excellent; everything is going as planned.
—Count Dooku and Darth Sidious
The first battle of the Clone Wars occurred after Separatist forces captured Obi-Wan Kenobi on Geonosis and charged him with espionage. Anakin Skywalker and Senator Padmé Naberrie attempted to rescue Kenobi, but were also captured and sentenced to death. A Jedi strike team led by Mace Windu stormed the Petranaki arena, where the prisoners were to be killed. The ensuing battle resulted in the deaths of many Jedi and the bounty hunter and template of the clone army, Jango Fett.
The Jedi managed to hold their own for some time, but were beaten back by the enormous amount droid forces. Rejecting Count Dooku's offer of surrender, the Jedi prepared to fight to the death, the clone army, under Jedi Grand Master Yoda's command, dropped from the sky in Republic gunships. After rescuing the Jedi from the arena, the clones engaged the droid army on the fields of Geonosis.
The battle on the surface was not the only conflict; in the space battle, the clone pilots, led by Adi Gallia, destroyed valuable Trade Federation battleships, and in the subterranean battle, fought between clone commandos—most notably the commandos of Delta Squad—and Separatist forces, saw victory for the Republic due to the annihilation of Separatist foundries and Geonosian leaders, such as Sun Fac.
Dooku, seeing that the battle was lost, took the plans for the Separatists' Ultimate Weapon and fled to a secret hangar. Intercepted by Kenobi and Skywalker, he managed to best them both, even severing Skywalker's right arm at the elbow.
Traveling to Coruscant, Dooku met with Darth Sidious at The Works. It was clear to the two Sith Lords that, while the Battle of Geonosis was a defeat, it was merely the first move in a much larger game.
Year One (11—12 ArS)
It is essential that the war endure for as long as possible; neither side can be allowed to end this war so quickly.
—Darth Sidious, to Count Dooku
Although the Battle of Geonosis resulted in a Republic victory, a war between the Republic and the Separatists was now inexorable. Millions of clone trooper units departed Coruscant on missions to find and defeat the CIS. The clones were led in these missions by the Jedi Knights—it was the first time that the Jedi Order had universally taken up arms since the Seventh Battle of Ruusan, nearly a thousand years prior.
Following the battle on Geonosis, Jedi Knights Sora Bulq and Tholme were dispatched to one of Dooku's bases, this particular one on Bakura, to confront him. Unfortunately for the Jedi, Dooku killed Bulq, though Tholme managed to escape. Seven days after the Battle of Geonosis, Mace Windu sent two Jedi, Aayla Secura and Ylenic It'kla, on a mission to Corellia to find the Techno Union scientist Ratri Tane, who possessed valuable information. Unexpected help came from Corellian Jedi Master Nejaa Halcyon, having just returned from a failed mission to put an end to the Sons and Daughters of Freedom in the Sluis sector.
This was followed by a Separatist/Trandoshan invasion of the Wookiee homeworld of Kashyyyk. There, the Trandoshans captured countless Wookiees and sent them off to concentration camps. Though the Republic managed to drive the Trandoshans off, war would continue to rage on Kashyyyk.
Witnessing the beginning of war, the Wookiees started the Decimator for the Grand Army of the Republic in the Erediss system and Alaris Prime. Its existence was learned by Bogeega Be'Daay, an operative who informed the Hutt Cartel and Boorka the Hutt; Boorka knew that the information would be fruitful to him if he gave it to the Separatists.
Year Two (12—13 ArS)
Like fire, across the galaxy, the Clone Wars spread.
Year Three (13—14 ArS)
I fear the dark cloud of the Sith shrouds us all.
Year Four (14—15 ArS)
If this war is to be won, it will be won in the outer rim.
Year Five (15—16 ArS)
A labyrinth of evil, this war has become.
Ending Campaigns (16 ArS)
The galaxy waited in anxious anticipation, wondering which side would make the final, daring move.
—Journal of the 501st, 16 ArS
At War's End
Is this peace? Has it been so long that we've forgotten what it feels like?
—Obi-Wan Kenobi, to Anakin Skywalker
Billions dead, countless planets devastated, and all for what? The limitless ambition of a single man who wanted to rule the galaxy because he thought himself superior to others?
—Padmé Naberrie Skywalker, to Anakin Skywalker