I'd base it more on the inklings of EU nonsense we got on the Clone Wars from the Thrawn trilogy and partly on what Lucas did with the Prequels already. Firstly, everyone assumed the Clone Wars and any Prequel would take place farther into the past then it actually did (more then the twenty or so years between the founding of the Empire and the events of Episode IV: A New Hope).
Shooting from the hip here so to speak and scribbled this up over the past two days.
Episode One: The Phantom Menace
For a thousand years, the Jedi have ushered in an era of peace for the Republic, ever since they vanquished the Sith in the Battle of Ruusan.
Padme Amidala is a Republican Consular Official being escorted to Tatooine, part of a "Commission" to investigate the claims of a 'Droid Army' threatening the Outer Rim. Part of her escort are two Jedi Knights, Qui Gonn Jinn and his padawan Obi Wan Kenobi. Also along with them is a Republic Military official... his name is uhhh... Panaka. He's Mandalorian. Since the Republic is gay and doesn't have a formal military but instead just local defense fleets/forces, they employ mercenaries sometimes and Mandalorians are some of the best and most reliable.
They arrive on Tatooine to meet the Planetary Governor who blames the Hutts for Droid sponsored Raids that are devastating the countryside or whatever and he wanted troops to defend the settlements, not a Senatorial delegation. The Jedi don't trust the Governor and neither does Padme but they decide to go meet the Hutt in charge after Padme contacts Senator Palpatine, her Boss who approved the Commission. The Hutt in cahrge can be found, of course, at a Swoop Bike race at the Boonta Eve Classic and the Mos Espa Stadium.
There, as official guests of the Hutts, they meet the Hutt who says that the purpose of the Swoop Race is to celebrate how the Hutts defended all of Civilization from the Droid Armies of Xim the Despot and that the Hutts don't have any interest in Droid armies and certainly wouldn't be employing them. As they watch the race, Padme Amidala is smitten (and vice versa) by a young Swoop Rider named Anakin Skywalker. At the end of the thrilling and super cool race, an Army of Droids suddenly attacks, attempting to Kill the Republican delegation and the Hutts. Anakin Skywalker (and his hulking Reptilian mechanic friend named Justin-don't laugh) rescue the Republican Delegation from the Droids and they escape Mos Espa.
They have to escape Tatooine, make their way back to the Republic, and figure out the Governor must've betrayed them for some reason. They confront the Governor but he escapes when a new sort of Droid, armed with a Red Lightsaber of the Sith, intercepts them. The Droid is designed in a manner of a Samurai (or ancient Sith Warrior) and is all black armored, looking very Vader-esque. They manage to defeat the Sith Droid and attempt to pursue the Governor when they are intercepted and apprehended by Mandalorian forces under Mandalorian General Jaster Mareel working on behalf of the Republic. It turns out the Chancellor of the Republic sent them.
The Jedi are shocked the Republic is working against them and sending mercenaries to do their bidding instead and the Mandalorians point out that while they are Mercenaries, they are honor bound to serve their Employers. Who do the Jedi truly serve? They also don't trust the Jedi since despite their powers, they were unable to discern the Governors true intentions and his deception. They also failed to save the Hutts. And with the Sith involved, the Republic doesn't want the Jedi involved any deeper then they already are. It might've been a millenia ago but they plunged the galaxy into enough Civil Wars. This is the Chancellors reasoning.
With the help of their Mandalorian Companion Panaka, the Jedi break out of their confines and find the Mandalorians are good bounty hunters... they tracked the Governor to Ruusan.
Ruusan, the sight of the last Battle between Sith and Jedi.
They arrive and find the Mandalorians attack them and soon discover they are possessed/corrupted by the Sith spirits and dark side energy that permeates this place. There's a momentary scare as the non-Force Sensitives among them are almost corrupted, but they all resist and Anakin Skywalker's further potential in the force is recognized. They head to the battlefield, the so-called Valley of the Jedi and then realize the Governor has been meat puppeted by a thousand year old Sith Lord who was slain by the Jedi in the Battle of Ruusan a thousand years ago. When the Republic arrives with reinforcements minus any Jedi, the Sith will corrupt them, sentients and powerful enough droids alike.
The Jedi and friends manage to defeat them. Qui Gonn Jinn is slain. Obi Wan Kenobi and Anakin Skywalker battle the Reborn Sith, when Anakin's Lizard friend Justin is slain and enraged, Anakin manages to strike down the Sith Master, channeling his latent force ability to do so and put an end to the madness before the Republic forces arrive. Obi Wan is disturbed, but also recognizes the potential. Leaving such potential unguided would be dangerous. He wants to train Anakin. Senator Palpatine congratulates them all, Anakin specifically, for their heroism and bravery. And as the Jedi Liaison to the Chancellor Master Dooku and Masters Yoda and Mace Windu discuss things, Senator Palpatine gazes at the Sith battlefield... his face stoic in the darkness.
Episode II: Attack of the Clones
Chancellor Valorum has been removed from office, voted out and now Chancellor Palpatine, with the support of the Jedi, is the new Chancellor of the Republic. Padme Amidala is a Senator of the Republic now and a powerful ally. Anakin Skywalker is training to be a powerful Jedi. There's a schism in the Republic. The Mandalorians and Jedi are still at odds and Master Mace Windu doesn't trust Anakin after hearing about the Duel in the Valley.
There's a schism in the galaxy. Despite being voted out of office, Senator Valorum is now a leader of the "Imperialist" faction, a group of Republic Governors and the Mandalorians who are distrustful of the Jedi and want to expand the Republic military, centralizing it under control of the Regional Governors and not on the whims of a Coruscant bound Senate. The Mandalorians support this. They also want to expand Republic authority to the Outer Rim, bring civilization there and end things like smuggling, the spice trade, slavery etc. Many Governors agree because it will increase their own power and domains and the influx or expansion of Senators would actually weaken the Senate ironically enough and stretch Jedi resources. There's brushfire wars all along the Outer Rim as the Governors dispatch their Local Fleets and Forces to "battle bandits and slavers" but actually are resource grabs. One of the most eager Governors is that of the Corporate Sector Authority.
A terrorist attack on Coruscant threatens Senator Amidala and the 'Peace' Faction and is believed to be fomented by the Imperials. For safety, they should leave Coruscant. Master Dooku suggests Naboo but Master Windu says it should be somewhere less known and open to Republic control and observation. So Master Windu, Mando Captain Panaka, Padawan Anakin and Senator Amidala head to Tatooine.
On Tatooine, Anakin and Padme bond as Anakin takes Padme to all of his old stomping grounds, meets his Mother, and Mace Windu learns from his Mother that he was conceived by the Force potentially and not to tell him. They also meet Owen and Beru, his normal Cousins or whatever. As they're hanging out there, suddenly SITH ATTACK! That's right, a small group of Sith suddenly strike at the ol' Lars Homestead and they have to defend themselves. Master Windu notices that the Sith don't seem to be trying to kill Anakin Skywalker for some reason. Then one of the Sith slays Anakin's Mother and Anakin dark side rages, pwning the Sith and making Master Windu truly disturbed. For Sith Knights, they were actually easy to kill, Master Windu then states. Panaka and Amidala then realize these Sith are clones.
Jedi Knight Obi Wan Kenobi and Jedi Master Dooku meanwhile head to some cool lush Outer Rim planet known as Wayland. There they find the terrorists were dispatched by one of the Imperialist Factions. A Governor of the Corporate Sector Authority. They do some investigating, and some battling and then discover the massive cloning facility the Corporate Sector Authority has secretly created. They defeat the CSA, capturing one of its leaders who they attempt to use 'aggressive negotiations' with but the Man kills himself with a grenade before he can say anything more then that "Sidious will do worse than kill him."
They then have a debate over destroying the Cloning Facility with Obi Wan arguing they are sentient lives and Master Dooku arguing they will be used for Evil and against the Republic. Obi Wan wants to inform the Republic and do this right. He manages to send a message out to Anakin who is to send a message to the Jedi Council. A group of Corporate Sector Mercenaries (make them Echani or something), training in anti-Jedi tactics, capture them both before they can destroy the Clones as Obi Wan instead states they should've.
Anakin and company get the message and send it to the Council, and then evade and trick Master Windu, leaving him behind to set off on a rescue mission. They arrive on Wayland but the CSA's Echani mercenaries ambush them and the heroes realize that Master Dooku is the traitor, the one who told the Imperials that they were on Tatooine. He also made the CSA leader blow himself up with a force triggered grenade before he could reveal his Master. He must be a Sith. They attempt to capture Master Dooku but Dooku defeats them both and takes Senator Amidala hostage when Master Windu, Yoda and the Republic Military loyal to the Senate arrive and start kicking ass.
UNTIL the SITH Clones are released. We get an awesome battle with the Senatorial Republic fighting Corporate Sector Authority ships. On the ground we see Jedi and Republic forces fighting Echani, Sith Clones and Clone Troopers. Master Dooku is bested by Yoda and Master Dooku threatens to kill Senator Amidala, using her as a hostage again. Anakin arrives, holds a saber to Dooku and tells him to let her go. Dooku asks for Amnesty. If he's promised amnesty, he'll let her go. The Jedi agree. He lets Amidala go and Anakin promptly executes him.
The Battle overall is looking bad though. There are a LOT of clones when suddenly Senator Valorum and his new Star Destroyers and Stormtroopers arrive and save the day. It turns out they are loyal to the Republic after all and blast the Clone forces to bits. Chancellor Valorum is hailed as a Hero of the Republic.
Palpatine's days are seemingly numbered. Anakin and Palpatine vow to support each other. Master Windu meanwhile... is very concerned.
Episode III: The New Order
The Clone Wars are tapering down. Now Grand Admiral Valorum and his new Imperial Army and Navy are battling the Clone Forces under their new Commander, General Grievous, a heinous General trained in the Lightsaber arts by the traitorous Master Dooku himself. Chancellor Valorum and his Armies are chasing the Clone Forces down in the Outer Rim. With them are the veteran Master Obi Wan Kenobi and Master Yoda. It's been years of War now and as they fight on some Outer Rim Planet, taking out a Trade Federation Governate or something when they discover that the Clone forces are no longer in the Outer Rim defending their most important sites. It's a feint and the Republic Army and Navy have been pulled away from the Core Worlds.
Serving as Chancellor Jedi Liaison, Anakin Skywalker, now a Knight, suddenly notices as does the entire planet, that the Clone's Main Armada has arrived over Coruscant itself and begins bombarding the planet in preparation for invasion. At the Chancellory, Palpatine urges Anakin to do what is right. Anakin contacts Senator Amidala, ordering her to evacuate the Senate chambers before he goes to help Captain Panaka, the new leader of the Chancellors Guards (in cool red cloaks) re-activate the planetary shields which they do. Only then do they find that the Clone forces have already landed and are striking both the Jedi Temple and the Senatorial Chambers (which has been evacuated).
That is until he receives a message that his Wife is still in the Senatorial Chambers. Apparently Grand Admiral Valorum is ordering forces to defend the Senatorial Chambers from the Invaders and let the Jedi stand and fight on their own. Master Windu orders Anakin to go to Jedi Temple and defend the Younglings and shit.
His wife is pregnant. He goes to rescue his wife in the Senatorial Chambers, cutting through the Clone Forces and then fins Grand Admiral Valorum is basically holding Senator Amidala hostage. He will not yield her to the Jedi. Anakin needs to do his duty and defend the Chambers and the Republic, and be a good soldier and follow orders. Anakin force blasts the good Admiral and rescues his pregnant Wife, getting her on a Speeder out of there when he notices from the speeder pad the Jedi Temple is destroyed by the Clone forces. At this very moment, Admiral Valorum says he's putting Anakin under arrest.
Anakin frags the Good Admiral and a few dozen of his accompanying bodyguards and stormtroopers when one of the Chancellors Guards reveals Chancellor Palpatine has been captured by the Clone forces and brough back to Grievous' flagship.
Master Mace Windu meets up with Anakin Skywalker and while he doesn't trust him he says they'll deal with his tardiness later. Along with Captain Panaka they all take to space to take on General Grievous and put an end to the Clone threat once and for all, fighting his way aboard Grievous' flagship. Captain Panaka goes to rescue the Chancellor while the Jedi confront General Grievous and after a prolonged and cool Battle, Grievous begs for amnesty. Mace Windu stops Anakin from executing him, having heard that before. Why would Grievous ask for that?
Grievous replies it was what he was told he would be given by Darth Sidious while cackling. Before he can say more, Chancellor Palpatine arrives and crushes Grievous heart. Mace Windu realizes that Palpatine is Sidious and Sidious replies everything he has done is for the good of the Republic. There's a bit of banter, then Mace Windu strikes at Sidious and they duel. Long story short, Master Windu is winning when Anakin says that he must be taken alive. Master Windu refuses, throwing Anakin's hypocrisy in his face and is about to strike him down when Anakin intercedes nonlethally. Momentarily distracted, Mace Windu is then lighting blasted by Chancellor Palpatine who fries Master Windu. Anakin is horrified.
They then see on a nearby console a broadcast is issued revealing Master Skywalker "assassinating" Grand Admiral Valorum. The stormtroopers accompanying Master Yoda and Obi Wan attempt to apprehend them but they evade the authorities. General Jaster Mareel, the same Mandalorian from Episode I, states he's taking over Republic military forces and all Jedi are to be apprehended on sight... and if they resist, executed for attempting to overthrow the Republic military.
Chancellor Palpatine says that they must put an end to these Warmongers once and for all and how everything he's done was for the good of the Republic. Anakin refuses, saying he must arrest the Chancellor. If he's Sidious, he's the one who told Dooku to foment the Clone Wars in the first place. before he can make a choice it's then revealed a force of Mandalorian Death Troopers are approaching Senator Amidala's residence, presumably to look for Anakin. Anakin races to rescue her, leaving the Chancellor behind. On the way out, he meets up with Captain Panaka and he comes along.
They confront General Mareel and his elite Mandalorians. The General says that Anakin is under arrest for the Murder of the Grand Admiral. Anakin doesn't talk and defeats the Mandalorians and their General in full view of his wife. His Wife asks what's happening and Anakin says that the Admiral Valorum and General Mareel betrayed the Republic and... and.. Chancellor Palpatine is trying to save it and tells her to stay here, where she's safe.
Anakin realizes, or believes, Sith Lord or not, this is the best for the Republic.
Obi Wan and Yoda head back to the Core Worlds, hunted by bounty hunters, Republic Imperial forces and Clone forces as well. Arriving on Coruscant they then realize Jedi are still being hunted and then make contact with Captain Panaka who tells them everything. About Anakin and Admiral Valorum, Master Windu and his death and Palpatine being a Sith Lord. When asked why he betrayed the Chancellor, Captain Panaka replies he's loyal to the Republic, not the Chancellor. They decide to approach Senator Amidala and tell her what's happening.
They decide to smuggle her out of Coruscant while Yoda will confront the Chancellor and Captain Panaka and Obi Wan protect the Senator. They'll use the underground tunnels over the incinerators. Republic forces detect them however, the Senator is being tracked and they get split up. Senator Amidala flees with Captain Panaka as Obi Wan fends off a group of bounty hunters. Captain Panaka and Senator Amidala suddenly come face to face with Anakin Skywalker and Anakin accuses Panaka of stealing his pregnant wife away from him. And how could he ever trust a Mandalorian.
Panaka tries to talk down his friend before finally giving in and stating that Anakin is just swallowing the Sith spit if he thinks anything he is babbling about is true. Padme tries to talk down Anakin but instead Anakin attempts to strike down Panaka. But the Mandalorian makes a fight of it. Using gas and flamers and other weapons, he puts up a spirited struggle before Anakin uses dark side powers, blasting Panaka with force lightning. Panaka dies as Padme is shocked when Obi Wan Kenobi comes upon them.
Obi Wan Kenobi tells Anakin he's fallen to the dark side and betrayed the Republic without even realizing it. Anakin says that the Jedi are weak. He learned from Darth Sidious, his new master, how Obi Wan refused to destroy the Cloning facilities and could've prevented this war. How the Republic and Jedi refused to deal with Chancellor Valorum earlier on and could've put an end to this before it began. It was the weakness of the Republic he grew up with on Tatooine... and that original traitorous Governor. And so on and so forth. The Sith were the boogey man for the Jedi for too long. Padme tells him he is wrong. The Republic and the Jedi maybe flawed but- Anakin lashes out at Padme with the Force, seriously injuring her, cursing her for choosing Obi Wan and the Mandalorian over him.
The duel begins, fighting over the Coruscant furnaces. It ends as expected with Anakin burning up and Obi Wan whisking Padme Amidala away. She's still alive... and even though he calls for her, she's too mortified at what he's become. What he believes in. For killing Captain Panaka, their friend. And letting their other friends die. And almost killing Obi Wan. And striking at her... in anger. He calls for her even as she is helped away from the area by Obi Wan. They abandon him to his fate.
The Yoda-Palpatine fight occur with Palpatine recreating the 'Valley of the Jedi' in his new Chancellory, using the captured Jedi as batteries and drawing off of their Force Powers so he can become a Dark Force God. Yoda destroys the horrific complex, releasing all of the Jedis spirits so that Palpatine can't use it but fails to kill Palpatine himself. It's a success, but only partial. Palpatine will not become a Force God, but he will rule the Republic.
Padme Amidala survives... but the wound is mortal... in that combined with the pregnancy of the twins... she has a terminal condition. She won't live for but a few years in seclusion and sadness but safety. Her Twins will be split up of course.
Anakin Skywalker recovers... and hunts down the Jedi... looking for his Wife. His children. He doesn't know if they are alive or dead, but with the forces of the new Imperial Republic behind him, he is a most useful instrument for Chancellor Palpatine. Over the coming years and decades... he endures more injuries, more wounds, battling Jedi and more and eventually becomes Darth Vader, placed in a suit of armor like that of the Ancient Sith from Episode I.
No Mandalorians were harmed in the development of this prequel trilogy.
TLDR
> Amidala is an actual Consular Official with skills. Obi Wan meets Anakin Skywalker after he's established himself as a skilled pilot and the like.
>
Episode I deals with an Ancient Sith who uses Sith Corruption to possess ancient Sith Vaderdroids and regular droids to lure the Republic onto the Planet of Ruusan where an ancient battle took place a thousand years ago. Anakin, thanks to his force heritage and potential, helps defeat them.
> Chancellor Valorum is replaced by Chancellor Palpatine who backs the Jedi and Padme Amidala. He also learns of the Valley of the Jedi.
>
Episode II establishes the characters a few years later. Schism with the Republic between Senatorials and Imperialists (under ex-Chancellor Grand Admiral Valorum).
> Master Dooku, Liaison to Chancellor Palpatine, and Master Kenobi investigate the Imperialist backed Corporate Sector Authority and their cloning ops. They disagree over destroying it when Echani Mercs capture them both.
> Imperialists attempt to kill Senator Amidala. She is taken to Tatooine for safety but alongside Windu and Anakin but is threatened by the Imperialists again. Anakin Dark Side PWNS these Imperialist Sith clones in front of Amidala again and Mace Windu for the first time.
> They then try to rescue Obi Wan (minus Mace Windu) only when they find them, Dooku betrays them, revealing himself as 'Darth Sidious?' The Republic and Jedi Order then show up, both Imperialist and Senatorial forces. Anakin executes Dooku.
>
Episode III has the Clone Wars are going on. Master Yoda and Kenobi are on the Outer Rim to finish the War when Clone Masters leader General Grievous attacks Coruscant why the Republic is away. The Jedi Temple is destroyed, Chancellor Palpatine captured. Admiral Valorum attempts to arrest Anakin Skywalker for attacking him to rescue his pregnant wife. Anakin kills him instead.
> Master Windu and Anakin head up to Grievous' flagship, defeat General Grievous and rescue Palpatine. Palpatine reveals he is a Sith Lord and kills Master Windu. Anakin is conflicted.
> Imperialist Republic Forces confront Padme Amidala in an effort to find Anakin. Anakin kills them all. He then agrees Palpatine has it right.
> Imperialist Faction Hunts Jedi to "arrest" them and Obi Wan and Yoda sneak back to Coruscant. Obi Wan attempts to smuggle Padme Amidala away when Anakin confronts them. Anakin in a rage injures his wife before getting fried. Obi Wan and Padme escape.
> Yoda confronts Palpatine, sees he's using the captured Jedi to become a Dark Force God Valley of the Jedi style. Yoda ends that plot but is defeated and escapes.
>> I managed to insert a Mandalorian good guy and bad guy for all three Episodes, go me!