Once upon a time in a galaxy far way, a mad scientist discovered a way of injecting alien DNA (MIDICHLORIANS!) into the neural tissue of cloned children, warping their growth and lifespan, but creating in their misshapen bodies awesome powers. In defiance of Republic law, which decrees clones are the legal children of their creators, the scientist continues further, fusing clone brains into cyborg bodies, making of living beings mere machines to be programmed and controlled. (The Trade Federation robot soldiers.)
The galaxy recoils in horror at the revelation.
That is, most of the Galaxy does. The outer Rim planets, where the welts of slavery still smart, and where most of the clones’ powers are flatly unneeded, public opinon wants him destroyed. The civilized worlds are also against it, but from a different angle: they want the clones destroyed. Raising the stakes, a handful of advanced prototype clones escape (accidentally killing dozens), and flee to sympathizing Naboo to beg aid and shelter.
Anakin Skywalker, now a junior Jedi Master, is sent to retrieve the escaped clones. He presents them a choice: to stand trial for murder—by extention granting their siblings legal status—or death.
The integrity of the Republic is called into question as the matter goes before the tribunal. The full might of the Jedi are needed ensure the safety of jury, witnesses, and judge as the fate of half a billion clone intelligences hangs in the balance.
Padme, representative of Naboo and leader of the Neutral Bloc (Federation assassins have eliminated the others), is sent to the vote. She knows that when she leaves Naboo she is going to her doom and that deals made are about to come due. For love and pity of Padme, her faithful servant, the Queen arranges for Anakin Skywalker—the Chosen One and the prophesied Healer—to protect her.
The Separatist faction makes the pro-clone position their line in the sand. The Remain faction frames their side of the issue as the rule of law: murder, theft, and destruction of property. (Anakin himself has definite opinions on property: it should stay put. However, he works for Padme).
The Jedi are deeply split and the Order lacks the ability to convince or compel its members to obey. Many simply leave–Obi-Wan among them.
Palpatine/Sidius has ordered Padme to vote Against. He has also called in his second bargain—her child with her choice of his lieutenants, Maul or Tyrannus. Palpatine’s plan is to force the Separatists into action, and trigger a short victorious war. Padme votes as ordered—but flees the Sith apprentices in terror, determined to die first. She can’t outrun her destiny, however, and Anakin convinces her to come with him, to the Separatist army, instead.
When the Senate overrides the jury and orders the clones terminated regardless of the trial, sympathetic worlds send ships to protect them. Shots are fired. The war begins.
The Separatists withdraw from the Republic and, aided by sympathetic Jedi, fight to free the clones. The Centrist planets, militarily weaker, react by consolidating their political power (aka, forming a central dictatorship), and counterattacking. Amid this dangerous landscape, the Sith are a shadowy presence, cutting deals and killing politicians, spying, sabotaging, informing, torturing. The war ravages from planet to planet.
Obi-wan Kenobi is a Separatist general; Anakin commands an elite flight squadron, his callsign Starkiller. (“I knew your father….”)
Some time into the war, Anakin confesses to Padme that he is in part responsible for starting it: he hates the clones as he hates himself, and his offer to them was false: he knew that the Senate would order their deaths, no matter what the courts decided. In atonement, he throws himself into the fight with renewed vigor, leading a reckless raid to the heart of Centrist territory, landing on the clone planet to rescue the remaining children and destroy the factories.
The mad scientist meets an appropriately ironic end in the rubble.
Anakin is covering the evacuee column when an attack fatally cripples his ship. As he is in the middle of his signature slingshot maneuver, the momentum, unchecked, will drag him into the sun. Trapped inside a dead ship, his screams, curses, prayers are heard by many others through the Force—and then, as his ship passes out of view into the brightness, go finally silent.