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The Clone Wars brought
about the end of the Jedi Knights "religion."
Jedi Knights used the force to keep the galaxy in some
kind of check. But increasingly during the Separatist
Crisis, many star systems wanted to secede from the Republic,
forming the Confederacy of Independent Systems. (CIS).
The wars seem to be
the brainchild of a dark Lord Sith. The first offensive
starts when Jedi Knight general attacks the Separtist's
new army of battle droids.
The Clone Wars drag
on for three years under Separatist leaders Count Dooku
and by the droid General Greivous. At the Republic's capital
city Coruscant the Clone Wars will be decided once and
for all by Order 66 that calls for the Great Jedi Purge,
a Separatist Massacre on Mustafar, and the establishment
of the Galactic Empire.
For two years before
the Clone Wars there was unrest amongst the Trade Federation.
The Republic sent two of its Jedi Knight to negotiate:
Jedi Master Qui-Gon Jinn and his apprentice Obi-Wan Kenobi.
situation and negotiate with the Trade Federation.

But it's all a trap to murder the two Jedi under orders
of Darth Sidious, a Sith Lord. The Jedi Knights escape
to Naboo, run by Queen Amidala. A ragtag Alliance of Naboo,
Gungan (underwater folks) and the Jedi win the day. Jedi
Master Dooku resigns from the Jedi Order in disgrace returning
home to Serenno.
This Trade Federation
under control of the Nemoideans, blockade the small planet
Naboo and demand capitulation by its queen, Padmé
Amidala. She ignores them and ask for protection from
he Galactic Republic who are supposed to be in charge
of the Galaxy.
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A relative peace holds
for about ten years until the Trade Federation try to
assassinate Senator
Padmé Amidala. Jedi Knights Obi-Wan and Anakin
Skywalker are on the case and dig up Jango Fett; inter-galactic
bounty hunter.
Meantime, Count Dooku
has fallen under the control of a Sith master Darth Sidious,
who begins organizing a Separatist coalition of planets
and civilizations to secede from the Republic. Their big
weapon: relentless unwielding battle droids. Thousands
of them.
Tracking Jango Fett
to Kamino, Obi-Wan discovers that Kaminoans have used
Fett's DNA to clone a vast army of soldiers. These Clone
Troopers were demanded by Jedi Master Sifo-Dyas.
With the Confederacy
of Independent Systems declared and secession a reality,
the Republic Senate deliberates over legislation: namely
one Military Creation Act, calling for the formation of
a special army to serve the Republic to stop any more
abandonment of the Republic. 
The
somewhat simple minded Shadow Senator for Naboo Jar Jar
Binks proposes the Chancellor Palpatine be granted Emergency
powers to resolve the stalemate in the deliberations.
Thus opening a slippery slope for further Government shenanigans.
Of course, this temporary measure lingers. The Battle
of Geonosis marks the start of the
Clone War, and the factory producing all these fierce
and relentless battle droids.
To up the ante Chancellor
Palpatine pretends to be kidnapped from Coruscant under
the command of the cyborg General Grievous. The Chancellor
is rescued and Confederacy leader Count Dooku killed by
Jedi Knights Obi-Wan and Anakin Skywalker.
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But
the threat wasn't real, but Anakin is sucked in to believe
he is worthy of Palpatine's respect. This
helps feed Anakin's inferiority complex about Kenobi trying
to hold him back in the Jedi Academy and stop him becoming
a Jedi Master. The Outer Rim Sieges and a number of battles
across the galaxy are stretching the Jedi Commanders thin.
Since Jedi Knights
are human and not clones, their battle prowess is highly
regarded. During the Battle of Utapau, Obi-Wan strikes
down General Greivous thus bringing the CIS to its knees..
Anakin
is left behind on Coruscant and learns the outwardly helpful
Palpatine is also Darth Sidious, Sith leader of the CIS.

Anakin informs Jedi Knight Mace
Windu, who comes to arrest the two-faced Chancellor. Now
Anakin has to choose or lose. Palpatine promised him unlimited
power to save his wife Padmé from death. As a Jedi
Knight Anakin is not as respected as he thinks he should
be. He cuts Windu's lightsaber wielding hand off, allowing
Palpatine gain the upper hand. Palpatine/ Darth Sidious
promote Anakin to Darth Vader. And the rest is Episodes
4,5 and 6. Well, almost.
Citing "the attack"
by Mace Windu as a call for action, Palpatine issues Order
66. All Clone Troopers are to execute their Jedi commanders.
Darth Vader leads the raid on the Jedi Temple killing
everyone they can. Only a few survive: Yoda and Obi-Wan.
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