Ok, I wasn't really sure where to put this, its just my tiny 2 cents on how the prequels should have unfolded, I don't dislike the prequels, but I think they could, and should have been a lot better than they are, I'm not sure if this is classified as fiction, but thought this would be the best place for this...
  This takes elements of the original script, and edits them, as well as adding in additional things, which I think would make the film better - be warned, things become more and more different as the films progress :xp: 
 The Phantom Menace   
 Turmoil has engulfed the
 Galactic Republic. A new 
 amazing energy source 
 has been discovered
 on the planet Naboo.  
 This has ignited a brutal competition 
 to gain the rights for its mining.
 Hoping to gain these rights
 the greedy Trade Federation 
 has blockaded the entire planet hoping
 to force the peaceful people of Naboo
 to sign exclusive trade rights
 to them. 
 While the congress of the
 Republic endlessly debates
 this alarming chain of events,
 the Supreme Chancellor has
 secretly arrived at the Jedi Temple
 hoping the Jedi may be able to
 resolve the dispute.... 
 (Queue customary opening shot of Supreme Chancellor ship entering Coruscant Space, and panning down over the planet, the Jedi Temple comes into view...) 
 The Supreme Chancellor arrives and is greeted by Master Windu and other Jedi Knights, and escorted to the High Council chamber, pass Jedi in training, fighting with lightsabers etc. Then in the tower the Jedi Council has convened to hear the leader of the Republic... 
 Yoda; “To see you Chancellor, good it is.. Troubling events on Naboo, there are” 
 SCV; “Indeed Master Yoda, thank-you for so quickly granting me an audience, this crisis has unfolded so quickly, I was somewhat taken a back by its speed. I do not know if the discovery of plasma tritium in the planet core of Naboo is a blessing or a curse.” 
 Mace; “What can you tell us of this discovery?” 
 SCV; “As you know, Naboo is a very unique world. Its water core is found no-where else in the known galaxy. Obviously the core is hazardous and extremely deep and they is why this discovery has only just been made. The Republic Scientists are amazed by the plasma tritium and its incredible power means size of space ships and stations may now be unlimited”.  
 Yoda “Greatly concerning is this development - as to the implication it could have, if one galactic entity were to gain sole rights.” 
 SCV “As ever Master Yoda you cut straight to the heart of the matter - It’s certainly in my opinion bad for the people of Naboo, though Chancellor Palpatine seems to think the discovery excellent for both his own planet and science. Regardless the senate is bogged down in debate and protocol and I find my hands tied. Could the Jedi dispatch some negotiators to end the blockade, and to sort out trade rights in the best interests of the people of Naboo and the Republic?” 
 Yoda “Send ambassadors for you, we will” 
 Mace “Thank-you for keeping us informed Supreme Chancellor Valorum, May the Force be with you”. 
 SCV “And with you” 
 The Supreme Chancellor Exits... 
 Yoda “Disturbance sense I in the force – there is more happening in the galaxy than aware we are. The Dark Side growing it is... A Phantom Menace, I sense Lurking. Sent, only the most gifted of Jedi Knights should be. Recommend Qui-Gon, do I” 
 Mace “Qui-Gon is a venerable, but a Maverick. Are you sure we should send him?” 
 Yoda “A proponent of the living force, one of the few – a talent I think need do we, to reveal what is happening on Naboo. Very knowledgable Qui-Gon is; know's Naboo best of all Jedi... Very gifted with a lighsaber also is he” 
 Ki-Adi-Mundi “Who else should we send?” 
 Yoda “Transfer my Padawan to Qui-Gon we should – Meditate on this disturbance in the force I must” 
 Mace; “Are you sure? Will Qui-Gon be a good influence on Obi-Wan? Can we trust Qui-Gon with the orders most gifted Padawan?” 
 Yoda “Unorthodox is Obi-Wan, and so shall his training be. A rebel Qui-Gon may be, but trust him do I. Good friends Qui-Gon and Obi-Wan are, very similar – both mavericks, much to learn they can from each other” 
 Mace “So the council is agreed? We Shall send Qui-Gon and Obi-Wan...” 
 Council agrees... 
 "Aye" "Aye" etc 
 Cut to Qui-Gon and Obi-Wan boarding their transport... 
 Qui-Gon "I look forward to completing your training Obi-Wan, I'm sorry Yoda has had to stop training you" 
 Obi-Wan "I'm sure Master Yoda has his reason, and it was an honour to be trained by him, I look forward to learning from you master" 
 Jessop (a Jedi Transport plot (aka Morgan Freeman) "Qui-Gon, sorry I won't be able to take you on this trip, family problems I'm affraid" 
 Qui-Gon "I sense that you not being a long on this trip maybe for the best, old friend" 
 Qui-Gon and Obi-Wan board transport... 
 Cut to Jedi Transport arriving at Trade Federation fleet... (standard script here...) 
 (From; 
http://www.blueharvest.net/scoops/pm-script.shtml) )  
 PAN DOWN to reveal a small space cruiser heading TOWARD CAMERA at great
 speed. PAN with the cruiser as it heads toward the beautiful green planet of
 Naboo, which is surrounded by hundreds of Trade Federation battleships. 
 INT. REPUBLIC CRUISER - COCKPIT 
 In the cockpit of the cruise, the CAPTAIN and PILOT manoeuvre closer to one
 of the battleships. 
 QUI-GON : (off screen voice) Captain. 
 The Captain turns to an unseen figure sitting behind her. 
 CAPTAIN : Yes, sir?
 QUI-GON : (V.O) Tell them we wish to board at once.
 CAPTAIN : Yes, sir. 
 The CAPTAIN looks to her view screen, where NUTE GUNRAY, a Neimoidian trade
 viceroy, waits for a reply. 
 CAPTAIN : (cont'd) With all due respect for the Trade Federation, the
 Ambassadors for the Supreme Chancellor wish to board immediately.
 NUTE : Yes, yes, of coarse...ahhh...as you know, our blockade is perfectly
 legal, and we'd be happy to recieve the Ambassador...Happy to. 
 The screen goes black. Out the cockpit window, the sinister battleship looms
 ever closer. 
 EXT. FEDERATION BATTLESHIP - DOCKING BAY - SPACE (FX) 
 The small space cruiser docks in the enormous main bay of the Federation
 battleship. 
 INT. FEDERATION BATTLESHIP - DOCKING BAY - SPACE 
 A PROTOCOL DROID, TC-14, waits at the door to the docking bay. Two WORKER
 DROIDS, PK-4 and EG-9 watch. 
 PK-4 : They must be important if the Viceroy sent one of those useless
 protocol gearheads to greet them. 
 The door opens, and the Republic cruiser can be seen in the docking bay. Two
 darkly robed figures are greeted by TC-14. 
 TC-14 : I'm TC-14 at your service. This way, please. 
 They move off down the hallway. 
 EG-9 : A Republic cruiser! That's trouble...don't you think?
 PR-4 : I'm not made to think. 
 INT. FEDERATION BATTLESHIP - CONFERENCE ROOM 
 A door slides open, and the two cloaked shapes are led PAST CAMERA into the
 formal conference room by TC-14. 
 TC-14 : I hope you honoured sirs with the most comfortable here. My master
 will be with you shortly. 
 The droid bows before OBI-WAN KENOBI and QUI- GON JINN.  
 OBI-WAN : I have a bad feeling about this.
 QUI-GON : I don't sense anything.
 OBI-WAN : It's not about the mission, Master, it's
 somethging...elsewhere...elusive.
 QUI-GON : Don't center on your anxiety, Obi-Wan. Keep your concentration
 here and now where it belongs.
 OBI-WAN : Master Yoda says I should be mindful of the future...
 QUI-GON : .....but not at the expense of the moment. Be mindful of the
 living Force, my young Padawan.
 OBI-WAN : Yes, Master...how do you think the trade viceroy will deal with
 the chancellor's demands?
 QUI-GON : These Federation types are cowards. The negotiations will be
 short. 
 INT. FEDERATION BATTLESHIP - BRIDGE 
 NUTE GUNRAY and DAULTRAY DOFINE stand, stunned, before TC-14. 
 NUTE : (shaken) What?!? What did you say?
 TC-14 : The Ambassadors are Jedi Knights, I believe.
 DOFINE : I knew it! They were sent to force a settlement, eh. Blind me,
 we're done for! 
 INT. FEDERATION BATTLESHIP - HALLWAY 
 A hologram of NUTE , surrounded by BATTLE DROIDS, appears in the conference
 room hallway. 
 NUTE : They must be dead by now. Blast, what's left of them. 
 The hologram fades off, as a BATTLE DROID, OWO-1, cautiously opens the door.
 A deadly green cloud billows from the room. BATTLE DROIDS cock their weapons
 as a figure stumbles out of the smoke. It is TC-14 , carrying the tray of
 drinks. 
 TC14 : Oh, excuse me, so sorry. 
 The PROTOCOL DROID passes the armed camp just as two flashing laser swords
 fly out of the deadly fog, cutting down several BATTLE DROIDS before they
 can fire. 
 INT. FEDERATION BATTLESHIP - BRIDGE 
 The bridge is a cocophony of alarms. NUTE and RUNE watch OWO-1 on the
 viewscreen. 
 OWO-1 : Not sure exactly what... 
 OWO-1 is suddenly cut in half in mid-sentence. RUNE gives NUTE a worried
 look. 
 NUTE : What in blazes is going on down there?
 RUNE : Have you ever encountered a Jedi Knight before, sir?
 NUTE : Well, not exactly, but I don't...(panicked) Seal off the bridge.
 RUNE : That won't be enough, sir. 
 The doors to the bridge SLAM shut. 
 NUTE : I want destroyer droids up here at once!!!
 RUNE : We will not survive this. 
 INT. FEDERATION BATTLESHIP - HALLWAY - OUTSIDE BRIDGE 
 QUI-GON cuts several BATTLE DROIDS in half, creating a shower of sparks and
 metal parts. OBI-WAN raises his hand, sending several BATTLE DROIDS crashing
 into the wall. 
 QUI-GON makes his way to the bridge door and begins to cut through it. 
 INT. FEDERATION BATTLESHIP - BRIDGE 
 The CREW is very nervous as sparks start flying around the bridge door.
 QUI-GON and OBI-WAN are on the view screen. 
 NUTE : Close the blast doors!!! 
 The huge, very thick blast door slams shut, followed by a second door, then
 a third. There is a hissing sound as the huge doors seal shut. QUI-GON tabs
 the door with his sword. The screen goes black as a red spot appears in the
 center of the blast door. 
 RUNE : ...They're still coming through! 
 On the door, chunks of molten metal begin to drop away. 
 NUTE : Impossible!! This is impossible!!
 RUNE : Where are those destroyer droids?! 
 INT. FEDERATION BATTLESHIP - HALLWAY - OUTSIDE BRIDGE 
 Ten ugly destroyer WHEEL DROIDS roll down the hallway at full speed. Just
 before they get to the bridge area, they stop and transform into their
 battle configuration. QUI-GON can't see them but senses their presence. 
 QUI-GON : Destroyer droids!
 OBI-WAN : Offhand, I'd say this mission is past the negotiaion stage. 
 The WHEEL DROIDS, led by P-59, rush the entry area from three hallways,
 blasting away with their laser guns. They stop firing and stand in a
 semi-circle as the smoke clears. OBI-WAN and QUI-GON are nowhere to be seen. 
 P-59 : Switch to bio...There they are! 
 The Jedi materialize at the far end of the hallway and dash through the
 doorway that slams shut. The WHEEL DROIDS blast away at the two JEDI with
 their laser swords. 
 OBI-WAN : They have shield generators!
 QUI-GON : It's a standoff! Let's go! 
 INT. FEDERATION BATTLESHIP - BRIDGE 
 NUTE and RUNE stand on the bridge, watching the view screen as the WHEEL
 DROIDS' POV speeds to the doorway. 
 RUNE : We have them on the run, sir...they're no match for destroyer droids.
 TEY HOW : Sir, they've gone up the ventilation shaft. 
 INT. FEDERATION BATTLESHIP - MAIN BAY 
 QUI-GON and OBI-WAN appear at a large vent in a giant hanger bay. They are
 careful not to be seen. Thousands of BATTLE DROIDS are loading onto landing
 craft. 
 QUI-GON : Battle droids.
 OBI-WAN : It's an invisible army.
 QUI-GON : It's an odd play for the Trade Federation. We've got to warn the
 Naboo and contact Chancellor Valorum. Let's split up. Stow aboard separate
 ships and meet down on the planet.
 OBI-WAN : You were right about one thing, Master. The negotiations were
 short. 
 Modified Script... Only real chance at this point, is the Queen is 36, and she has a 13 year old daughter... Padme. 
 INT. FEDERATION BATTLESHIP - BRIDGE 
 TEY HOW recieves a transmission. 
 TEY HOW : Sir, a transmission from the planet.
 RUNE : It's Queen Amidala herself.
 NUTE : At last we're getting results. 
 On the view screen, Queen Amidala appears in her throne room. Wearing her
 elaborate headdress and robes, she sits, with her only daughter, the teenage PADME and surrounded by her governorning council. 
 NUTE : (cont'd) Again you come before me, Your highness. The Federation is
 pleased.
 AMIDALA : You will not be pleased when you hear what I have to say,
 Viceroy...Your trade boycott of our planet has ended. 
 NUTE smirks at RUNE. 
 NUTE : I was not aware of such a failure.
 AMIDALA : I have word that the Senate is finally voting on this blockade of
 yours.
 NUTE : I take it you know the outcome. I wonder why they bother to vote.
 AMIDALA : Enough of this pretense, Viceroy! I'm aware the Chancellor's
 Ambassadors are with you now, and that you have been commanded to reach a
 settlement.
 NUTE : I know nothing about any Ambassadors...you must be mistaken. 
 AMIDALA, surprised at his reaction, studies him carefully. 
 AMIDALA : Beware, Viceroy....the Federation is going too far this time.
 NUTE : Your Highness, we would never do anything without the approval of the
 Senate. You assume too much.
 AMIDALA : We will see. 
 The QUEEN fades off, and the view screen goes black. 
 RUNE : She's right, the Senate will never....
 NUTE : It's too late now.
 RUNE : Do you think she suspects an attack?
 NUTE : I don't know, but we must move quickly to disrupt all communications
 down there. 
 INT. NABOO PALACE - THRONE ROOM 
 The Queen, her daughter Padme, Eirtae, Sache and her Governor, Sio Bibble, stand before a
 hologram of Senator Palpatine, a thin, kindly man. 
 PALPATINE : ...How could that be true? I have assurances from the
 Chancellor...his Ambassaodrs did arrive. It must be the...get...negotiate... 
 The hologram of PALPATIONE sputters and fades away. 
 AMIDALA : Senator Palpatine?!? (turns to Panaka) What's happening? 
 CAPTAIN PANAKA turns to his SARGEANT 
 CAPT. PANAKA : Check the transmission generators...
 BIBBLE : A malfunction?
 CAPT. PANAKA : It could be the Federation jamming us. Your Highness.
 BIBBLE : A communications disruption can only mean one thing. Invasion.
 AMIDALA : Don't jump to conclusions, Governor. The Federation would not dare
 go that far.
 CAPT. PANAKA : The Senate would revoke their trade franchise, and they'd be
 finished.
 AMIDALA : We must continue to rely on negotiation.
 BIBBLE : Negotiation? We've lost all communications!...and where atre the
 Chancellors Ambassadors? How can we negotiate? We must prepare to defend
 ourselves.
 CAPT. PANAKA : This is a dangerous situation, Your Highness. Our security
 volunteers will be no match against a battle-hardened Federation army.
 AMIDALA : I will not condone a course of action that will lead us to war. 
 EXT. SPACE LANDING CRAFT - TWILIGHT (FX) 
 Six landing craft fly in formation toward the surface of the planet Naboo. 
 EXT. NABOO SWAMP - SHALLOW LAKE - TWILIGHT 
 Three landing craft slowly descend through the cloud cover of the
 perpetually gray twilight side of the planet. One by one, the Federation
 warships land in the eerie swamp.
 OBI-WAN's head emerges from the mud of a shallow lake. For in the
 background, the activities of the invasion force can be seen in the mist.
 OBI-WAN takes several deep breaths, then dissapears again under the muddy
 swamp. Troop Transports (MTT's) emerge from the landing craft. 
 EXT. NABOO EDGE OF SWAMP / GRASS PLAINS - TWILIGHT (FX) 
 The droid invasion force moves out of the swamp and onto a grassy plain.
 OOM-9, in his tank, looks out over the vast ARMY marching across the rolling
 hills. A small hologram of RUNE and NUTE stands on the tank. 
 RUNE : ...and there is no trace of the Jedi. They may have gotton onto one
 of your landing craft.
 OOM-9 : If they are down here, sir, we'll find them. We are moving out of
 the swamp and are marching on the cities. We are meeting no resistance.
 NUTE : Excellent. 
 EXT. NABOO SWAMP - TWILIGHT 
 Key point... No Jar-Jar! 
 Qui-Gon runs through the strange landscape, glancing back to see the
 monstrous troop transports, emerging from the mist. Animals begin to run
 past him in a panic. 
 The two troops fire laser bolts at OBI-WAN. QUI-GON deflects the bolts back, and the STAPS blow up. One-two. OBI-WAN is exhausted and tries to catch his breath. 
 OBI-WAN : Sorry, Master, the water fried my weapon. 
 OBI-WAN pulls out his burnt laser sword handle. QUI-GON inspects it, as  
 QUI-GON : You forgot to turn your power off again, didn't you? 
 OBI-WAN nods sheeplishly. 
 QUI-GON : (cont'd) It won't take long to recharge, but this is a lesson I
 hope you've learned, my young Padawan. 
 Qui-Gon "We must find the Gungans, despite the animosity they feel towards the Naboo, we will need their help if we are to get to Theed" 
 Obi-Wan "But master, we are in the middle of the forest, where are these Gungans?" 
 Qui-Gon "They live in magnificent cities under the water, don't expect a warm welcome though, they dislike outsiders, follow me" 
 Obi-Wan; "Don't worry, this has not been our day for warm welcomes." 
 Qui-Gon and Obi-Wan dive under water, and swim to the Gungan city...
 They arrive and run into Gungan security... 
 Qui-Gon "Take me to your leader" 
 Obi-Wan "Well, that was original, Master Yoda would never say something like that" 
 Qui-Gon "Would you have preferred me to say 'To your leader, take me?" 
 Both laugh... 
 Standard scene minus Jar-Jar... 
 INT. OTOH GUNGA - HIGH TOWER BOARD ROOM 
 The Bosses' Board Room has bubble walls, with small lighted fish swimming
 around outside like moving stars. A long circular judge's bench filled with
 GUNGAN OFFICIALS dominates the room. OBI-WAN and QUI-GON stand facing BOSS
 NASS, who sits on a bench higher than the others. 
 BOSS NASS : Yousa cannot bees hair. Dis army of mackineeks up dare tis new
 weesong!
 QUI-GON : That droid army is about to attack the Naboo. We must warn them.
 BOSS NASS : Wesa no like da Naboo! Un dey no like uss-ens. Da Naboo tink day
 so smarty den us-ens. Day tink day brains so big.
 OBI-WAN : After those droids take control of the surface, they will come
 here and take control of you.
 BOSS NASS : No, mesa no tink so. Mesa scant talkie witda Naboo, and no
 nutten talkie it outlaunders. Dos mackineeks no comen here! Dey not know of
 uss-en.
 OBI-WAN : You and the Naboo form a symbiont circle. What happens to noe of
 you will affect the other. You must understand this.
 BOSS NASS : Wesa wish no nutten in yousa tings, outlaunder, and wesa no
 care-n about da Naboo.
 QUI-GON : (waves his hand) Then speed us on our way.
 BOSS NASS : Wesa gonna speed yousaway.
 QUI-GON : We need a transport.
 BOSS NASS : Wesa give yousa una bongo. Da speedest way tooda Naboo tis goen
 through da core. Now go.
 QUI-GON : Thank you for your help. We go in peace. 
 QUI-GON and OBI-WAN turn to leave. 
 OBI-WAN : Master, whats a bongo?
 QUI-GON : A transport, I hope.