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Opening Crawl. Jist: the Republic has abolished slavery. In protest, the Niemodian slavers have prepared an attack on Naboo. The Jedi have secretly stowed aboard the tradefed vessels.
PAN DOWN to Naboo, with droid ships in orbit.
(Optional scene here where we see Qui Gon and Obi Wan drop out of ventilation shaft, observe the droid army, and discuss plans to stow away aboard landing ships.)
Landing ships head toward planet and land. (In some way we need to communicate that the tradefed plan is to attack Naboo from the Gungan side, enslave them first, then attack the Naboo. Also, Nute is not aware of the Jedi's presence.)
QuiGon saves Jar Jar, they encounter Obi Wan, and go to Gungan city. Jar Jar is surprised to see
that the city is deserted (rotoscope the city to be empty).
Meanwhile, the Gungans emerge from the swamp. Nute activates the droid army, and the battle ensues.
We cut to Gungan city exterior, as the Jedi and JarJar leave in a bongo.
Gungans fight and lose to Droid army.
A little exposition by JarJar in Bongo. He explains that the Naboo and Gungans don't get along. No other underwater footage.
Droid army rolls on to Theed, takes the city, and captures the queen. Nute mentions that the Gungans have been defeated and will be placed in concentration/slave camps. Nute says the Queen and her people are next.
Queen is lead away by droids, we suddenly see Qui Gon and Obi Wan appear and save them (we cut the Bongo's arrival at Theed, so we are surprised by the Jedi's appearance here). No mention of negotiations. Jedi take the queen to her ship and get off the planet.
Nute contacts Maul to track the Queen. She is needed to sign a treaty that will enslave her people.
Tatooine stuff (a whole other ball of wax).
Coruscant stuff (eh...)
They return to Naboo and have their briefing. The plan is to storm the city and capture Nute. At the same time, the pilots will disable the droid control ship. No mention of a Gungan distraction. (Why are they disabling the ship? As a backup to victory if the attempt to capture Nute fails, and to free the Gungans.)
*One question arises, going with MTHaslett's idea for a Gungan concentration camp (which I loved, by the way), what exactly will JarJar be doing in the end? I think we need to give him something to do. Should he try to sneak into the Gungan camp? Should he go talk to Boss Nass (who can be in hiding in the sacred place)?
End battles play out pretty much as usual (except no Gungans). Qui Gon dies first. Queen is captured next. Anakin ends up in tradefed ship. (Things are looking really bad at this point. The only thing that can save them is the force.) Then Qui Gon, already dead, uses force talk to help Anakin destroy the control ship (just like in ANH).
Ship blows up and gungans are freed, as we see droids fall over (as per MTHaslett's idea). And finally (I hope this can be pulled off as SomethingStarWarsRelated suggested), have the droids in the throne room fall over via rotoscoping. Queen: "It's time to negotiate a new treaty".
Palpatine's shuttle arrives and Nute is escorted away. Yoda talks to Obi Wan (but maybe this can be cut). Funeral scene (Obi Wan mentions that he will train Anakin).
Iris out to end credits.
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This still leaves the Queen's identity unresolved, but I think it works well otherwise. This whole queen identity subplot is really weak anyway. Why does Nute have any reason to thing Padme is the queen before her decoy shows up? She's not dressed as the queen.
Some possibilities for revealing the Queen:
1) Qui Gon can address her as queen or highness when she asks to come along on Tatooine. Some whimsical music can play this up.
2) Maybe the scene with Boss Nass in the sacred place can be salvaged. But what help is Padme asking for? I'm a bit stumped on this one. Any ideas?