Here is the synopsis for the cancelled Ep. II rewrite, as I promised.
Star Wars: Episode II - Knights of the Republic
Timeframe: 35 BBY (about five years after Episode I)
We begin on the surface of Nabu, in the new capital city of Hales. It is the fifth anniversary of Queen Amidala Naberrie's coronation, and there is much celebration in the streets, with a float parade moving down the main street of the city. On the top of the grandest float, Queen Amidala sits atop a regal throne, waving to the jubilant crowd around her. In a tall building overlooking the celebration, a single man crouches in a dark room, looking out through a small window at the celebration below. This man is an assassin, garbed in close-fitting black garb, with a sniper rifle aimed through the window at the Queen. The assassin calibrates his weapon, gets Amidala in his crosshairs, and then pulls the trigger.
The Queen is hit by the projectile, and she topples from the float to the ground below, dead with a hole through her skull. The shouts of celebration quickly turn to screams of horror. A few bystanders quickly make out where the shot originated from, and alert the authorities. The assassin, aware that his cover has been blown, quickly jumps to his feet, and sprints from the room. As he climbs down a few floors, he is greeted by a retinue of armed policemen. They open fire, and the enemy jumps through the nearest window, shattering the pane of glass and falling the remaining stories to the ground. He hits the ground hard but survives relatively unscathed, though his leg is badly sprained. He gets to his feet and begins to hobble away, pulling out a blaster to ward away anyone who tries to get in his way.
The assassin comes to an alley, but as he ducks into its shadowy depths, a large figure lunges out. A mechanical arm goes out, colliding with the assassin, knocking the blaster out of his hand and throwing him off his feet. From the alley steps a large mechanical skeleton, white with a white cloak and skull-like face containing yellow, reptilian eyes. This is the remains of the Kaleesh warrior Qymaen jai Sheelal, resurrected in the form of a cyborg killing machine.
The assassin moves quickly, pulling a second blaster out from a concealed holster, but the cyborg is quicker. With lightning speed Sheelal steps forward, and sends one of his solid metal feet crashing down on the man's hand, smashing it and the blaster underfoot. The assassin howls with agony, and desperately begins trying to pry his ruined arm out from under the Kaleesh's heel.
Sheelal takes his foot off the enemy's shattered hand, then seizes the man's head in one of his large durasteel hands, lifting the man up, allowing him to flail helplessly in the air. At that moment a young woman, garbed in the uniform of a regular Nabuan bodyguard, comes stepping around the corner. This is the true Queen Amidala, the Queen killed by the assassin being a decoy. Seeing the assassin trapped in the Kaleesh's grip, she immediately begins telling him to free him, to let him live. The cyborg gives the Queen one look, then closes his fist around the enemy's head. The wet sound of bone disintegrating flies through the air, and the assassin's body spasms once with death, then goes still. The enemy dead, Sheelal drops the corpse to the ground. Frozen with horror, Amidala just stands there, and the cyborg leaves the scene, ignoring the Queen completely as he steps past her.
We now move to another planet, the world Concord Dawn. This area of the planet is very rainy, with thick grey cloud cover hovering over a surface of muddy plains. Through the sky streak several Republic gunships, moving towards a point on the horizon. The ships soon come to their destination, a large stone citadel protected by a battalion of Mandalorians. The gunships land and open up, spilling their soldiers to the ground, Anakin Skywalker and Obi-Wan Kenobi among them. The Jedi activate their lightsabers, and soon the battle between the Republic forces and the Mandalorians is joined.
The two sides battle fiercely, and the two Jedi, skilled though they are, find the Mandalorians very capable adversaries indeed. Regardless, the Republic soldiers begin to overwhelm the Mandalorians. Soon the battle is over; the citadel is taken and most of the Mandalorians are either dead or captured.
The Jedi then enter the citadel. They make their way through the passages and corridors of the structure, finding no Mandalorians to block their way. They enter a turbolift, and take a ride down to the lowest level of the building. Once they step out, they find themselves in a vast laboratory housing countless transparisteel cylinders containing gestating beings. The citadel is a Mandalorian cloning facility, and Obi-Wan and Anakin have come to appropriate it for the Republic.
As they move towards the panel that controls the functions of the cloning cylinders, they find that the tanks have been taken off-line, and that if power isn't restored immediately, the clones will die. Anakin quickly tries to restore power, but nothing works.
At that point a Mandalorian, encased in pure white armour, steps out from the shadows, revealing himself to the Jedi. He holds out a plastic circuit board, and tells the Jedi that without it, the cloning cylinders cannot be brought back online. At that point he places the card in a pouch strapped to his side, then pulls out a lightsaber, activating its purple blade. At that point the Jedi activate their own lightsabers, and a fierce duel begins. In the end the Mandalorian is slain, and Obi-Wan quickly retrieves the card from his person; placing the board back in its proper place in the panel, power is soon restored to the cloning cylinders. Anakin pulls the helmet from the dead Mandalorian's head, revealing him to be a clone of Mace Windu. The clone is somewhat younger than his template, with close-cropped black hair and a barcode tattooed on his forehead. The apprentice makes a joke about how Windu shouldn't lend his image to inferior products, and Obi-Wan scolds him light-heartedly.
The story moves forward with Obi-Wan and Anakin being sent to Nabu to guard Amidala from a radical political movement that wants to see her dead. It is here where we are introduced to Cos Palpatine, the son of Grand Vizier Dantius Palpatine and Amidala's closest confidant.
As the Jedi guard the Queen, she and Anakin begin to get closer. He eventually shows her the lightsaber he built, revealing that its unique cyan glow comes from the crystal pendant she gave him years ago, which he installed within its inner workings. Obi-Wan notices the growing bond between them, and cautions Anakin about getting attached to her.
Eventually, the radical faction after Amidala sends another assassin to kill her, but the Jedi stop him in time; unfortunately, this assassin is killed by palace guards before the Jedi can get any information out of him.
Soon, Amidala reveals to Anakin that she is no longer the true ruler of Nabu, that the Parliament of Nabu - governed by Grand Vizier Palpatine - have taken complete control of the planet and ushered in a totalitarian rule, placing the cyborg Qymaen jai Sheelal as her caretaker, that she has been left as little more than a figurehead with no real power, and that the faction targeting her is a Nabuan liberation movement. Anakin takes this information to Obi-Wan, but Obi-Wan says their job is to protect the Queen, that the Council will not allow interference with the planet's system of government. Anakin begins to argue, but in the end he begrudgingly decides to go along with Obi-Wan's orders.
Soon, the Jedi Council makes contact with Obi-Wan, telling him that he must leave Nabu and join Jedi Master Jard Dooku on a mission to the edge of the Galaxy, into Kaminoan territory, where they must destroy a gravity generator that enables stable hyperspace travel between the Kaminoan galaxy and Republic space. Before Obi-Wan leaves, he admonishes Anakin again not to get involved with the conflict between the Liberators and the Parliament. Anakin tells him he won't go against him. After Obi-Wan leaves, though, Amidala begins trying to convince Anakin to disobey his master, to help her and Cos slip out of the palace and join the Liberators. Anakin refuses, but his conscience begins to eat away at him. Eventually, the young Jedi decides to make contact with the Jedi Council themselves to obtain permission to help overthrow the Parliament. The Council refuses to grant him permission, though, echoing Obi-Wan's earlier sentiments. With this, Anakin decides to disobey the Council, and he decides to dedicate himself totally to Amidala and the Liberators.
Meanwhile, Obi-Wan and Dooku - along with several other Jedi - have finally arrived at the edge of the Galaxy. Waiting for them, though, isn't just the Kaminoan gravity generator, but a whole Kaminoan fleet as well. The Republic ship is boarded, the crew captured, and soon Obi-Wan along with the other Jedi find themselves on a journey into the heart of Kaminoan space. Here we learn that Dooku has been secretly harbouring resentment towards Obi-Wan for years, who he blames for the death of his old apprentice Qui-Gon Jinn.
Back on Nabu, Anakin along with Amidala and Cos have managed to ally themselves with the Liberators. Soon a coup is underway, and the Liberators are in open conflict with the Parliament. It is here that Anakin takes his first major step toward the dark side. As the Liberators and Parliament forces battle, Anakin and Amidala finds themselves at the mercy of the Kaleesh Qymaen jai Sheelal. Anakin quickly moves to defend the Queen from the cyborg, who unsheathes a pair of lightsabers he bought off the black market. As the two combatants battle, it becomes clear that the cyborg is the stronger of the two; Sheelal begins to wear Anakin down, taunting him as he strikes several painful blows. As one of the Kaleesh's lightsabers carves a nasty gash into the flesh below one of Anakin's eyes, he mocks the Jedi one final time, remarking that his unique cyan lightsaber will make an excellent addition to his collection. At that point Anakin opens himself to the dark side of the Force, and with restored strength, begins to turn the tables on the evil cyborg. With powerful rage, Anakin begins to push Sheelal back. Soon, the Jedi cuts away both of the cyborg's arms, then cuts him down. He begins slashing down at the fallen cyborg with a berserker rage, carving the Kaleesh into pieces as Amidala screams at him to stop.
We now near the end. Obi-Wan and Dooku have escaped the Kaminoans and have returned to the Galaxy - their friendship now severely tainted - and the coup on Nabu has been successful; Dantius Palpatine along with his fellow Parliament members have been arrested and are awaiting trial, and a new government is in the process of being formed.
Anakin's involvement in the coup is discovered by the Jedi Council, and he is soon taken to speak before them. Anakin unhesitatingly rebukes the Jedi, condemning them for their complacency and lack of empathy. In the end the Council declares Anakin a Jedi no longer, and Mace Windu himself orders the former apprentice to relinquish his lightsaber to him. Anakin angrily turns away from the Council member, and instead goes to Obi-Wan instead, telling his master that he is the only Jedi whom he still respects and the only one who can have his lightsaber. Obi-Wan accepts the lightsaber, and Anakin leaves the Council chambers with his head held high.
Later, back in the palace on Nabu, Anakin tells Amidala about his excommunication from the Order, and that he can now devote himself completely to the restoration of Nabu's government. At that point a courier walks in, presenting a small plastic cylinder to Anakin. Thanking the courier, Anakin takes the container and unscrews the top, dumping its contents - his lightsaber - into his open hand. Anakin exchanges glances with Amidala, then looks the saber over. Smiling wistfully, he returns the saber to his side, clipping it on his belt.
A few months pass, and the former Nabuan Parliament members have all been found guilty of crimes against the people and have been sentenced to life in prison. At one of these prisons is Dantius Palpatine, housed in a small cell and garbed in drab brown prison coveralls.
Through an intercom Palpatine is told he has a visitor, and the cell door opens, allowing his son Cos Palpatine accompanied by a pair of guards to step through. Dantius quickly leaps up from his bunk, grabbing his son by the front of his tunic and slams him up against the wall, calling him a traitor. At that point a mechanical beep comes from the younger Palpatine's throat, followed by an emotionless computer voice that begins a short countdown. Dantius quickly realizes this isn't his son, but a human replica droid with a built-in bomb.
The bomb goes off, reducing Palpatine, the guards, and every other nearby living being into dust, and blows a massive hole in the wall that opens outside. From atop the roof of a nearby building stands a dark figure - the Sith Lord Maul, alive and well. His face grim, he watches flame blaze from the gapping hole in the prison's side, then turns around and walks off.
Elsewhere on Nabu, Anakin and Amidala sit together in a lush field, the sun blazing down around them. They are both very happy, and are talking about the happy future of the world around them. As they continue to talk about the burgeoning new government, though, Anakin reveals that he has his own vision for Nabu's future, one far darker than Amidala's. As his word begins to appal Amidala, the sky grows overcast, violently swirling with dark clouds. At that point Anakin vanishes, and this scene is revealed to be a dream.
Amidala begins calling out for Anakin, demanding to know where he's gone as she climbs to her feet. As she turns around, she comes face-to-face with a towering Gothic cathedral. Hoping to find Anakin within, Amidala enters the dark depths of the titanic structure.
As she makes her way along the damp, mildewy cathedral walkway, Amidala begins to hear the faint sound of lightsabers clashing in the distance. As she moves closer toward the sounds, she soon finds the source; Anakin, with a crimson lightsaber, engaged in fierce duel with a figure in dark armour, robes, and cloak. Amidala watches as the dark figure wears Anakin down, and screams out when he cuts the former Jedi down.
Amidala runs over to the fallen man's side, and cradles his still form as she begins to cry. As she weeps, the dark figure moves closer to her, bringing his lightsaber up close to his face. As the cyan light plays over his enshrouded face, revealing a disturbingly familiar nose and chin, deep, almost mechanical, breathing begins to issue from his lungs.
At this point Amidala bolts upright in bed, out of her nightmare and awake. She breathes heavily, sweat pouring down her face. She wipes a few strand hairs away from her face, and when she looks out, she sees Anakin stand out on the balcony leading out of the room, his back to her. She gets up out of bed and joins Anakin on the balcony. As he turns to her, they both smile. She then moves over to his side, and places her head on his shoulder. Together they look out over the Nabu countryside, watching the bright new sunrise together. The end.