A sorcerer/mad scientist who serves the Dark Side has somehow found out the secret of cloning, and makes clones of several murdered Jedi Knights to lead enslaved worlds in an insurrection against the Republic. Jedi Knights are as strong as superheroes in the Galaxy and strong enought to control their own army. They will be stormtroopers flying in Star Destroyers. In response, the real Jedi Knights and the Galactic Senate form a volunteer army to combat the invaders. The sorcerer is after one of the rare treasures of the Jedi Knights, the Kaiber crystal. Because of it's peaceful nature, care has been given to King Bail Organa of Alderaan to guard over it. The crystal, is an unlimited fuel source for a fleet of ships and can make a Force wielder almost invincible. This conflict will become known as the Clone Wars.
Upon hearing of the war's start, a seventeen year old refugee on the backwater world of Tatooine named Anakin Skywalker runs away from his brother Owen's farm to join the Galactic Star Fleet. Both of his parents were killed by the sorcerer Mandolorian in a massacre that nearly anihilated the agricultural world where he and Owen once lived. He wishes to avenge their deaths and is especially fond of the stories of a certain thirty-five year old general named Ben Kenobi who is the youngest in his ranks.
After several years of training, Anakin becomes quite a skilled pilot and one of his maneuvers saves Alderaan from invasion by the Jedi clones who killed his parents. For his bravery, he is recognized by King Bail Organa and General Ben "Obi-Wan" Kenobi in a ceremony. General Kenobi notices how strong Anakin is in the Force and takes him on as his apprentice to help him achieve his goal of winning the war. Yoda would've advised against it because Anakin was too bitter and angry, and being a general in war Obi-Wan could not devote all the time he needed to to train his apprentice. The two retrace the path of the clone fleet to a top secret cloning facility in the Outer Rim where and the secret behind the mystery Jedi is revealed.
By the second film, the war is going badly for the Republic, despite the destruction of the clone facility at the hands of General Kenobi and Anakin. More worlds are captured and a massive invasion overruns the Republic. Anakin has married the senator of Alderaan, who would have appeared in the first film, and at the time of their honeymoon, she kidnapped by the cloned Jedi general. The Kaiber crystal has since been hidden on a volcanic planet by Lady Skywalker, its guardian. Ben has neglected Anakin's training due to the war and misses the surprise attack on the palace which results in Lady Arcadia being kidnapped. Master and apprentice pick up the trail of the senator together searching for the source of the new clones too, fighting many units along the way.
Eventually, the two friends manage to track the Jedi clone to the right planet where he is trying to force Lady Skywalker into the protection chamber of the magic crystal. Both Jedi engage him, but Anakin acts on rage and tries to kill the clone in cold blood. Fearing his apprentice will fall to the Dark Side if he does, Ben directly intervenes with his lightsaber and accidentally knocks an irrate Anakin down. He tries to block Anakin from fighting on, and causes Anakin to think he has betrayed him. The clone escapes and Anakin is furious at the assumption his master has betrayed him to steal the glory kill for himself. Both Jedi duel dangerously close to a volcano erupting around them and Ben ACCIDENTALLY knocks his apprentice into a molten pit leaving him near dead and totally scarred. Due to the dangerous volcano, Republic forces retreat into hyperspace and the crystal is lost to Imperial forces, the war with it as well.
About nine months later, the war has turned on the Republic even more and the Galaxy's infrastructure has been almost utterly destroyed. Strangely many of the Jedi leaders have been mysteriously killed in the short amount of time, like before, but no new clones have appeared. In the time between movies, as Ben grieves the apparent death of his apprentice at his hands, he leads a raid on a prison planet where Lady Skywalker has been held and rescues her, killing the evil clone who took her in reprisal. To his surprise he finds that she is pregnant with Anakin's child and she is taken to Galactic City (Coruscant) away from the fighting. Ben then gets visions through the Force of a new rising evil behind the scenes and speculates his apprentice may be alive.
The Jedi Elders meet secretly, but are all eliminated by a mysterious dark cloaked assasin. As Ben probably goes to Degobah to meet with Yoda about the death of his apprentice, he senses the sudden murder of thousands of Jedi at the hands of a single bladed assassin. In a surprise attack, Imperial forces storm Galactic City and surround it. Several senators are arrested and imprisoned in the Presidential palace, including Lady Skywalker. Jedi Knights respond to the Emperor's challenge to rescue the capital, and some return to their home world for an emergecny session.
Ben senses an even grander conspiracy to overthrow the Republic, he teams up with King Bail to rescue Lady Skywalker and then sneaks her to the Jedi homeworld where he thinks she will be safe. In secret he heads to the Jedi homeworld where the Jedi are just returning home from combat. Legions of stormtroopers under the leadership of a familiar dark robed cyborg march in and open fire, killing most after a long, drawn out battle.
Ben and a psuedo-Vader, who is only wearing a breathing mask and the cloak at this point, duel. During it, while Anakin is physically unrecognizable, Ben senses his identiy and finds out that his apprentice has been injured but also become a Manchurian candidate of sorts after secret military experiments by the Imperial forces made him into a cyborg after he fell into the molten pit where he was burned alive and kept alive in a secret labratory run by Republic black ops. A group of secrety conspiring military leaders and big business interests secretly started the war in the hopes of turning the Republic into a police state, with the the Senate President at the helm. Vader is a mix of being, brain injured, brainwashed, and ignorant from being kept isolated by his bosses. He has been convinced that Ben tried to kill him on the volcanic world to take the glory of recovering the Kaiber crystal for himself and in jealously of his apprentice's great abilities.
Lady Arcadia who was on site of the attack and was exposed to a near lethal dosage of radiation during the fighting, gives birth to Luke and Leia in secret on Alderaan, but does not die and is instead disguised as a maidservant to work in the palace of King Bail under his medical care. She will die about the time Luke and Leia turn three so that Leia has some memory of her.
Ben takes Luke to Anakin's brother Owen on Tatooine out of guilt for causing Anakin to first run away because of his delusions of grandier years before and for having further broken up the Skywalker family, but failing his training and permanently destroying him on the volcanic planet. He will also make sure Anakin's dream that his son gets training in the Force comes true.
With his victory complete, the Emperor gathers his clone Jedi generals for a celebration ending the war, where they are all slaughtered and disposed of by Lord Vader. Instead they are replaced by non-Force users as grand moffs. Through a twenty year period of reconstruction, civil war, and nationalization of commerce in the galaxy, the new Galactic Empire's growing central authority will slowly continue to control all ways of life until the Imperial Senate is abolished and regional governors take their place about the time a newly finished Death Star is ready to enforce their tyrannical rule. But we already know how that's going to work out for them...
