Perhaps the story doesn't need to be done vastly differently than the prequels to have no spoilers. As I've posted incarnations of this story elsewhere, this will be draft three of an evolving set of ideas forced into formation. Make of it what you will:
It is a time of galactic war. Vicious cloned warriors, striking from the Great Rift, have attacked the Galactic Republic and are now moving directly to its heart. The bright center of the Republic lies exposed. Countless star systems lie in ruin.
The final hope for the Republic lies the hands of an ancient and powerful order of holy warriors - the JEDI KNIGHTS - who alone have the strength to repel the relentless clones. However, their venerable order is not what it once was. Few in the galaxy have faith in the Force - the mystical field of energy that give the Jedi their power - so the Jedi have dwindled in numbers and power. Like the embers of a dying fire roused to brilliance by a searing wind, they now fight desperately to regain their former glory.
The Jedi Knight Obi-wan Kenobi is among the fiercest of the order. Being the last student of an old master of the Force, he knows that the Jedi once took and trained disciples from an early age, and this gave them great numbers and power. But it also led to bitter dissent and rivalry, and strained the unity of the order. Yet Commander Kenobi has need of both of these things if the Republic is to survive the clones, and so when he sees the presence of the Force in one of his new recruits, he selects this young man - Anakin Skywalker - to fly with him against the clones in his newly formed fighter squadron.
Skywalker, he discovers, is only sixteen, having faked his identity to fight with for the Republic. Impressed both by his audacity and his skill as a pilot, Obi-wan decides to train Anakin in the ways of the Jedi. Anakin soon becomes a formidable warrior, learning quickly and bringing Commander Kenobi victory after victory for the Republic. Soon Kenobi is advanced to the rank of General, due in no small part to Anakin's heroics. However, Kenobi's reliance on young Skywalker takes its toll on the young man. Anakin soon tires of war, and falls in love with a woman from the peaceful planet of Alderaan, which is liberated from clone forces by Skywalker and General Kenobi.
Yet the war rages on, and there are personnel shortages within the military. Suddenly the Chancellor of the Republic is captured and taken to a clone stronghold, and so the Kenobi sends Skywalker in to rescue him. Anakin discovers that behind the clones lies a power which is a corruption of the Force, one that seems far more powerful. In the darkness of the clone stronghold, Anakin draws his laser sword against a mysterious warrior guarding the Chancellor, one who has this dark side of the Force as his power. The warrior seems to know the young Jedi's training, matching him move for move. Anakin cannot overcome this terror shrouded in darkness, and so he flees. The clones gain a decisive victory, and the Republic remains in mortal peril.
Anakin is haunted by his defeat by the mysterious warrior and his failure to rescue the Chancellor. He immerses himself in strategy and training, knowing every secret movement of Republic forces under the command of the Jedi knights. His mission is to find the Chancellor. However, every rescue mission turns into a rout. Jedi who should have lived now die. The Jedi suspect treachery in their midst, and so they turn to their bravest, whom they know to be Anakin, to seek out the traitor. Anakin knows that this traitor was once trained as a Jedi, perhaps even by Kenobi himself, for he knows Anakin's every technique. He is convinced that this traitor is the mysterious warrior he battled in the clone stronghold, but he cannot find this warrior among the Jedi.
Then Obi-wan discovers that the woman Anakin fell in love with is actually a clone. She was fighting on Alderaan but threw down her weapons and posed as a native of that world. Obi-wan asks her why she defected, as it is not in a clone's nature to betray their comrades. She explains that the DNA of the Clones is incomplete, and so they receive a genetically formulated antidote at their strongholds. Clones that do not will slowly weaken and die, and this is why they are so ferocious, with no defectors. They are literally fighting for their lives. Yet she would rather spend a few years in peace than a lifetime at war. But she is pregnant, and fears that she will not be strong enough to bear Anakin's child.
Meanwhile, the Jedi have discovered the location of the captured Chancellor, and they all mount a final attack on the primary stronghold. Kenobi and Skywalker are selected to lead the covert mission to rescue the Chancellor while the rest of the Jedi lead the ground and fighter attacks. But Anakin, mistrustful of Obi-wan and suspecting him of treachery, decides to go alone.
The final assault begins. As the Jedi and the Republic forces open a way through the massed clone forces, Anakin slips by, and winds his way to the very center of clone stronghold. There he finds the Chancellor, who is unguarded and surveying the battle from atop his tower. Surrounding him are six figures cloaked in red, seated as if watching the proceedings. The Chancellor bids Anakin watch the final destruction of the Jedi, and Anakin realizes that the Chancellor is the mastermind of the war. Anakin demands to have the genetic antidote, and the Chancellor responds:
"Whoever controls the antidote controls the clones, Anakin. If this is what you seek, here he stands, the antidote to all war."
"It's in you?"
"The Clones are me, young Skywalker. Incomplete without me, male and female I created them. They are my children. Do you know the true power of my family? It was my grandfather who first understood. His father was a Jedi, and he was strong in the Force. His son was strong in it as well, as was I. The Force chose our family above all others to rule the galaxy."
This is the first that any Jedi has heard of the Force being with an entire family rather than a single individual, and it shakes Anakin to his core. As starships incinerate each other in the blackness before him, the Chancellor continues:
"Though you are the greatest of the Jedi, you are not my son. Therefore it is time for you to meet an old friend, though you haven't yet been properly introduced."
The shadow warrior steps out of the blackness.
"Meet my apprentice, Darth Vader."
The warrior again fights Anakin, again drives him back.
"This is Obi-wan's greatest student. I have simply continued his training. Soon, Darth Vader will be a master of the Force, and shall join me as my loyal servant. That is, unless the great Anakin Skywalker can defeat him."
Anakin grows angry, and the warrior seems to gain power. Anakin attacks ferociously, hating this figure who betrayed and killed so many of his brethren.
"You killed Jedi! Because of you millions are dead! How can you remain silent? You will answer for this!"
The warrior yet advances, forcing Anakin back.
"Can you not see, Skywalker? Anger only makes my apprentice stronger."
Meanwhile, the battle rages. General Kenobi, who is in a Republic warship, orders an evacuation of the skeleton crew as the ship loses shields. He races to his personal fighter, but along the way runs into Anakin's wife, who had joined the cause as a gunner because of the lack of trained personnel. The ship breaks apart as they both escape in the fighter. They maneuver through the battle, and Anakin's wife realizes that Obi-wan isn't half the pilot that people think he is, for Anakin had been doing much of the heroics. The ship gets blasted and shields go down, but Obi-wan manages to take it to hyperspace.
Anakin takes one of the red-robed figures hostage. The Chancellor chuckles:
"How un-Jedilike of you, Anakin. You cannot defeat Darth Vader, so you threaten a woman."
The figure removes her mask. The Chancellor crows:
"These are some of my many daughters. With the blood of the Force, they will birth a dynasty that shall rule the galaxy forever."
Anakin is horrified to discover that they all have the face of his wife.
Meanwhile in hyperspace, Obi-wan realizes that Anakin's wife has taken a piece of shrapnel, and as he attempts to tend to her, she remarks on Obi-wan leaving the battle, claiming that it is cowardice. She says that she doesn't fear death, having made the choice to die when she defected. Obi-wan however still fears death, and always admired the way Anakin would brave all odds to save the day, risking his life countless times. But Anakin's wife shares a different story, saying that Anakin couldn't understand her reason for choosing death. Anakin in fact acted bravely because he secretly feared death, and didn't want people to think him a coward.
Anakin meanwhile stares at the face of what looks like his wife. As fear overcomes him, the darkness seems to deepen, and the shadow warrior approaches Anakin from behind. Anakin realizes that he has not the strength to defeat the Chancellor, nor even the ability to defeat Vader. He realizes that death awaits him. The Chancellor sees his resolve:
"You accept your death, Skywalker? You may be a Jedi yet."
"A Jedi never dies."
Vader swings his lightsaber, and the scene ends.
The Republic surrenders to the Clones and the Chancellor, now made Emperor. He addresses the Senate, claiming that in his mercy he has allowed it to endure, if only to serve his will. A black-robed figure stands beside him along with the new military cabal the Emperor has created.
Obi-wan and Anakin's wife survey the stars from space, adrift aboard a space station surrounded by the refugees of a thousand decimated worlds. Around them life finds a way to endure, as ships arrive and return to parts unknown.
