Author' Note: I know this is not technically what happens after the movies, but I'm ignoring the books. This is what I think would have happened. Be patient, this is a long story.
Disclaimer: I don't own the copyright to Star Wars, George Lucas does.
The Naboo Rebellion
Ensign Aldreaan Skye returned to the cockpit of his C-707 medium transport as the cruiser reached the Naboo atmosphere. He reached for the comlink.
"Theed Royal, this is Imperial Transport VIP 78009 requesting landing clearance for type 707 and escorts." He said, while simultaneously guiding the craft through reentry procedures.
"VIP 78009, this is Theed Royal, Cleared for type 707 on pad 4, escorts Hangar 1 for refueling," came the reply.
"Copy that, VIP 78009 out."
The young pilot was not only returning to his home planet to deliver the new governor, but to have his own conversation with the queen.
Aldreaan Skye was a native of Naboo, passionate about his teachings and interested in public service. But then came the war. He immediately joined the Galactic Republic Navy, only to be changed over to the Imperial Navy. He piloted transports and freighters for the year of war he was old enough to serve as an officer, and was now the pilot for Governor Neron, assigned to the Naboo system. He was not happy with the emperor for his political decisions.
As they neared the beautiful city, Skye and the escorts parted. He was used to hearing the roar of thrusters form the Eta-2 class Jedi starfighters, now he heard the terrible screeches of the V-Wings, a sign of the terror of the Empire.
The cruiser was guided to a smooth landing and greeted to a group of welcoming politicians. Queen Apailana and her advisors along with the Naboo Council were ready to greet whatever came out of the newly blue painted vessel. Ald felt uneasy to see the line of chrome-plated limousine speeders ready to carry them to the palace. The first two had too many blue markings for his likings.
Ald pressed the door key, and stepped out of the cockpit. He still felt uneasy being in public with this gray uniform. He felt people disliked him less in the old red of the republic. Governor Neron walked out first, then his chiefs of staff and finally the young pilot and copilot were shoved into the small police speeder at the rear of the motorcade.
The group slowly traversed the streets of Theed, watched by the terrified and angry faces of the Nabooins. Even the droids seemed uneasy with the passing line of vehicles. Ald turned to Ensign Syri Kenna, his copilot,
"This is my home planet, my home city and these people look at me like I'm the devil!" He said.
"The whole Empire idea doesn't sit well with anyone. The entire galaxy is uneasy. When will you talk to the queen?"
"Soon."
The group moved on to the palace, and the motorcade stopped. The entourage left the speeders and walked down the beautiful halls crafted by generations of regal and loving kings and queens, only to arrange for this Imperial drone, Vel Neron, to take it all over. The whole idea was too terrible for anyone to even think about.
"Your Majesty," Aldreaan said discreetly, "a word?"
"Let me occupy Governor Neron first, then yes."
Queen Apailana then led Neron to the throne room, where he and the council could discuss the matters of the galaxy without noticing the lack of their pilot or queen. Apailana then led Ald to her private office and showed him a seat.
"Your Majesty, I feel the need for you to decline Neron's offer. Naboo as been self governing for ages, there is no need for imperial interference."
"Ensign Skye, I am sorry, but I don't seem to have a choice. The Empire will destroy us if I don't."
"We are a peaceful system, and we have proven ourselves a vital part of the galaxy with Senator Amidala. It's also Emperor Palpatine's home system. We must risk the threats from the empire, we must try to remain independent"
"It is my wish to do what is best for the people of Naboo, and at the moment our choices are bad and worse, but I will try negotiations. If that doesn't work, you know what to do."
Ald then moved behind the desk, and pressed a button hidden under it. The weapons compartment Queen Amidala had installed then opened. He took a small chrome pistol and pocketed it.
"I'm ready for whatever happens, are you ready," He asked.
"Let's go, I want to get this over with."
The two then reentered the throne room, and Queen Apailana took the throne. The council took their seats, and the young pilot took his place with the guards. Neron began the proceedings, telling the group how the empire was willing to cooperate if they were, and how wonderful the empire was. He explained how there was no reason for them not to join and so on. The queen then had her word,
"Governor, Senator Binks tells me that the Emperor is taking power away form the senate, is this true?"
"Queen Apailana, I assure you that the Emperor's doings are for the good of the people, and that what he does is not meant to harm the public."
"Senator Binks feels that these decisions with the senate are in order to make the Emperor more like a dictator, and that these governors are to further his dictatorship dreams."
"Your Majesty, I feel that you do not agree with my coming, but I assure you Emperor Palpatine knows what he is doing and would not do such a thing. As for Jar Jar Binks, I feel that if he is saying these things, perhaps you should remove him from the Senate."
"Neron, I can take your suggestions up to a point, but to want Senator Amidala's best representative not to take her place, that is preposterous. I will not have you making a mockery of my people, or the gungan people in my throne room. The nomination of a senator is my decision, not yours. Keep in your place governor. I am still queen!"
"Jar Jar Binks is a fool! He, and the rest of his kind belong on some desolate outer rim planet, where I don't have to worry about them. Your Majesty, By the order of Emperor Palpatine, I shall take you place as ruler of Naboo. You are no longer queen."
At this point, Aldreaan removed the blaster from his uniform pocket, as did Captain Pananka, head of the queen's security. They advanced on Neron.
"Governor, I am asking you to leave peacefully, if you do not, my forces will have you executed right now. Until the queen signs the agreement, she is in charge," said Pananka.
"You wound not dare kill an imperial officer. Naboo would be exiled in a moments notice," responded Neron.
"There will be no need for exile, I, Queen Apailana Hereby declare the Sovereignty of Naboo independent from the Galactic Empire."
At this point, Neron reached for his holstered weapon. Ensign Skye and Captain Pananka both shot, both hit the target. Neron's body fell to the floor. The chiefs of staff immediately surrendered.
The Rebellion of Naboo was over in a matter of minutes. The system was free from the grasp of the Empire. Palpatine would not know of it for a matter of days, as the escort V-wings were shot down before they left the atmosphere. Queen Apailana was now the first queen of the Independent Sovereign Republic of Naboo.