TheBoilingChef's got me thinking about how I would do the PT. Here goes:
TPM:
-The galaxy is splintering. Dozens, maybe hundreds of worlds are breaking away from the Old Republic for a host of reasons, some like its grown too corrupt, too powerful, too bloated, inefficient, its overtaxing, or its playing favorites, etc. There is a political crisis on Alderaan. There is a coup on the planet, and the Jedi are sent to negotiate (Two Masters-Ben Kenobi and Dooku, and their Padawans-Anakin and Padme). They are escorting Prince Bail Organa, the leader of the government in exile, back home for the negotiations. The coup leader-Baron Sandage-is in league with Darth Maul (he might talk to Sidious offscreen but Sidious would not be seen in TPM, perhaps heard over an intercom link or something). Alderaan being a very prominent planet, close to Coruscant can't fall victim to the wave of secession in the eyes of Chancellor Valorum, but the coup leaders-disaffected nobles-have already made a deal with some of the Seps. They set up came and spring a trap for the Jedi. Dooku, a critic of the Republic-a reason he was chosen to negotiate-senses something afoot and decides to stay on Alderaan and get to the bottom of it. Obi, Anakin, and Padme escape with Bail. Darth Maul is ordered to capture or assassinate Bail. That is the price for the alliance. Sandage can't have a closer heir to the throne than himself left alive.
With the spacelanes blocked, Ben takes a roundabout way to Corellia, where he hooks up with his brother Owen, who wants nothing to do with the Jedi, but helps nonetheless.
Once they get back to Coruscant, after escaping Maul, they find that neither the Council nor the Senate want to help. Palpatine, a Senator from Alderaan, engineers Valorum's fall. But Bail rallies a group of friendly senators to his cause and they raise an army to take back Alderaan. Ben and the others decide to go back with them, to find out Dooku's fate and to discover more about Maul.
At the end of TPM, Bail's forces are repulsed and the Jedi believe Dooku has been killed by Maul. Ben later on kills Maul. Sandage is able to rally other worlds to his aid and the Confederacy is born.
AOTC: It is about four years later. To stop the Seps from conquering the galaxy, the Republic has hired Mandalorian mercenaries to help shore up the motley Rep forces. Mandos use clone soldiers. The mercs continue to raise their fees, eventually holding the Republic hostage. Palpatine and Bail began arguing for the creation of a clone army. Jedi are torn about whether to fight or not, as well as about a clone army. Of course the Mandalorians are opposed and they turn on the Rep. Ben, Anakin, and Padme do find out what happened to Dooku. He is now a key leader of the Seps. He believes that the Republic has fallen under the sway of Sidious and that only by dismantling it can the galaxy truly be free.
ROTS: Another three years later-the Clone Wars go on about 7 years. The Seps have Mando clones and the Reps have cloned soldiers too. It's a bitter, vicious war. Anakin kills Dooku in combat, striking a major blow to the Sep cause. Anakin and Padme have grown close. When she tells him she is pregnant, he knows they can no longer hide their illicit relationship. Anakin has grown closer to Palpatine at this time. Palpatine offers him a job as his Security Head. The Council has concerns, but can do nothing when Anakin quits the Order. Padme follows suit. As the war winds down, Palpatine is concerned about traitors amongst their midst, some even in the Jedi Order. Anakin is disbelieving at first, though he comes to see some Jedi do harbor anti-Palpatine views, and Anakin has come to see Palpatine and the Republic as synomous. The Jedi and some Senators have begun secret negotiations with the Seps to bring the war to a close. Palpatine convinces Anakin that they are plotting against the Republic and sends Anakin to arrest them. Things go wrong and Palpatine has the justification he needs to arrest the Jedi. Anakin is forced to pick a side and he chooses the wrong one, but for a 'noble' reason-to prevent continued galaxy-wide slaughter which he thinks will happen if the Republic is overthrown and the war is allowed to continue.