Over the past 4 years Obi Wan has reunited with Quigon the two have sparred he's amazed with his apprentice's new skills so they go to Nagato after 10 minutes of sparring Quigon is exhausted Obi Wan asks why are you so tired you're only 44 Nagato says it's not just his age it's his force reserves they're lower than yours are they can be increased with training but he's at a certain age that if I train him like I did you he wouldn't survive it Quigon says I can do it he puts Quigon through the same regiment as Obi wan except with Obi Wan here to help him train it will go faster also when it comes to lightsaber training Obi Wan is his sparring partner as Quigon just learns what Obi Wan was taught except the forms Quigon chooses are forms 1 ,2 and 4 however once they are done training Windu tells them that they have a mission and it may involve a battle Nagato says count me in this surprises everyone there as nagato hasn't left the temple since he came back from his meeting with the Sith almost 100 years ago.
Turmoil has engulfed the Galactic Republic the taxation of trade routes to outlying star systems is in dispute hoping to resolve the matter with a blockade of deadly battleships, the greedy Trade Federation has stopped all shipping to the small planet of Naboo while the congress of the Republic endlessly debates this alarming chain of events, the Supreme Chancellor has secretly dispatched three Jedi Knights, the guardians of peace and justice in the galaxy, to settle the conflict....
Everyone gets cleaned up Windu says if you're going on a mission then you can't go out in shorts he takes him to the jedi robes synsethsizer he picks standard jedi robes like what Windu is wearing but his will be orange the inner shirt and pants will be white the belt will be black as will be the boots and cloak seeing his choices Windu sighs but agrees then pays for the order he gets taken to a changing room once he walks out all eyes are on him Windu puts several things he will need in his belt like a lock pick communicator matches breather grappling hook hacking device and universal key to any ship once that is done and Nagato puts his belt on Windu hands him his lightsaber he meets up with Obi Wan and Quigon then they leave to go meet with their client.
On the way there Nagato says before we get there a couple of things as I'm sure that none of you two have been in a real war before Quigon says actually I have been in a couple of battles Nagato says good that will help but just so we're on the same page I'm in charge of this mission you two will be the public faces of the mission but you will do what I tell you also when it comes time to fight a Sith none of you are ready so that is my fight they both nod Nagato smirks then says however Quigon you will get a chance to test your skills against said sith sooner than you think on this assignment he asks how strong is he compared to us Nagato says about even in power but speed strength and skill level who knows they both nod in understanding and a little bit of fear.
Thirty-two years before the events of Star Wars: Episode IV A New Hope (thirteen years before the formation of the Galactic Empire), there is a trade dispute between the Trade Federation and the outlying systems of the Galactic Republic, which has led to a blockade of the Mid-Rim planet of Naboo. Supreme Chancellor Finis Valorum, leader of the Galactic Senate, has secretly dispatched two Jedi, Master Qui-Gon Jinn and his Padawan, Obi-Wan Kenobi, to serve as "the ambassadors" to the Federation flagship, in order to meet with Viceroy Nute Gunray and resolve the dispute. Unknown to them, the Trade Federation is in league with the mysterious Darth Sidious, Dark Lord of the Sith, who secretly orders Gunray to invade Naboo and kill the two Jedi upon their arrival. When Gunray asked if that would be legal, Sidious says that he would ensure that it was.
The Viceroy locks the Jedi in the meeting room and attempts to kill them with poison gas while having their ship, the Radiant VII, destroyed in the hangar, but they escape. After battling through squads of battle droids, Jinn and Kenobi make their way to the command deck where Gunray is located, shielding himself behind blast doors. The Jedi are forced to flee upon the arrival of two Destroyer Droids and stow away aboard two separate Federation landing craft leaving for the surface of Naboo to begin the invasion.
Back in the command deck, Queen Amidala contacts Gunray to express her disapproval of their blockade, with Gunray explaining that they wouldn't have done it without the approval of the Senate. When she asks about the ambassadors sent by the Chancellor, Gunray claims that they have received no such ambassadors, leaving Amidala startled and suspicious. Gunray ends communications with her and informs his aide that they should disable all communications on the planet.
Meanwhile, Amidala is conversing with Senator Sheev Palpatine regarding the recent attempt at negotiations and how Gunray claimed that they did not receive any ambassadors. Surprised, Palpatine states that he had assurances from the Chancellor that his ambassadors did arrive. However, Palpatine is unable to finish his sentence as his hologram flickers out. Naboo Governor Sio Bibble suspects that an interruption of communications is a sign that an invasion from the Trade Federation is imminent.
On the planet's surface, Qui-Gon saves native outcast Jar Jar Binks from being crushed by a Trade Federation MTT. Kenobi appears, pursued by STAPs, which are destroyed by Qui-Gon. Jar Jar Binks shows the two Jedi the way to an underwater Gungan settlement, Otoh Gunga. Meanwhile, the Trade Federation occupies Theed, the capital city of Naboo, and captures Queen Amidala along with the rest of the government. In Otoh Gunga, the Jedi meet the Gungan leader, Boss Nass, and ask him to help the people of Naboo, but Nass refuses due to hate of the people of Naboo and sends them off in a bongo submarine. They are attacked by an opee sea killer and a colo claw fish but both fish are eaten by a sando aqua monster. The Jedi, with Binks in tow, arrive in Theed and rescue Queen Amidala. They depart for Coruscant, the Galactic Republic's capital planet, to ask for help from the Senate. As they attempt to run the blockade, the queen's starship is damaged by Federation battleships, but an astromech droid named R2-D2 manages to repair it and they narrowly escape.
Due to the damage to the ship's hyperdrive sustained in the attack, the Jedi decide to land on the nearby planet Tatooine for repairs. While searching for a new hyperdrive generator, they befriend young Anakin Skywalker, a slave boy, whose master is Watto, a Toydarian junk dealer. Watto has the required parts in stock, but Qui-Gon is unable to purchase them, as Republic credits are worthless on Tatooine.
Anakin is gifted with piloting and mechanical abilities, and has built an almost-complete droid named C-3PO. Qui-Gon senses a strong presence of the Force in Anakin, and feels that he may be the Chosen One—the one who will fulfill a prophecy by bringing balance to the Force. By entering Anakin into a podrace, Qui-Gon orchestrates a gamble with Watto's chance cube in which "fate" decided that the boy alone, since Qui-Gon was unable to include the youth's mother in the bargain will be released from slavery while also acquiring the parts needed for their ship. The night before the race, Qui-Gon does a blood test on Anakin and discovers that the boy's midi-chlorian reading is off the chart.
Anakin wins the race (defeating his rival, Sebulba) and joins the team as they prepare to leave for Coruscant, where Qui-Gon plans to seek permission from the Jedi High Council to train Anakin to be a Jedi. Meanwhile, Darth Sidious sends his apprentice, Darth Maul, to kill the two Jedi and capture the queen. Maul appears just as the group is leaving the planet, and duels with Qui-Gon. The fight is cut short when Qui-Gon escapes his black-robed assailant by jumping on board the Naboo Royal Starship as it takes off.
On Coruscant, Qui-Gon informs the Jedi Council of the mysterious attacker he encountered on Tatooine, coming to the conclusion that his attacker is a Sith, the latter being a religious order who were followers of the dark side of the Force and thought to have been extinct for over a millennium, much to the shock of the Jedi Council. Qui-Gon also informs the Council about Anakin, hoping that he can be trained as a Jedi. After testing the boy and deliberating with one another, the Council refuses, deeming him too old for training according to the Jedi Code. They are also concerned that they sense much fear in the boy, and that he has a clouded future.
Meanwhile, Senator Palpatine meets with Queen Amidala to warn of corruption in the Senate and advises that she may have to call for a Vote of No Confidence in Supreme Chancellor Finis Valorum. When their petition to the Senate is refused, Amidala sees no alternative but to do just that. Palpatine is among the candidates to become the new Supreme Chancellor. The queen later announces to Palpatine that she will return to their home planet to repel the invasion of her people by herself. She is frustrated by the Senate's deliberation and lack of action, and feels that even if Palpatine is elected Chancellor, it will be too late. The Jedi Council sends the two Jedi to accompany the queen back to Naboo, hoping to shed light on any Sith involvement.
Amidala, back on Naboo, attempts to locate the Gungans at Otoh Gunga, but Jar-Jar, after searching the city, informs them that it has been abandoned. He then leads them to the Gungan Sacred Place, where he is certain the Gungans will be. The Gungans are initially distrustful, until the "handmaiden" Padmé reveals herself as the true queen and humbly begs for their help. She negotiates with Boss Nass to form an alliance and unite their peoples in battle against the Trade Federation. Captain Quarsh Panaka and several other security forces were also dispatched to rescue anyone imprisoned in the Trade Federation's prison camps, although they were only able to successfully extract a handful.
Next, Amidala informs Qui-Gon and Nass of her battle strategy: with the Grand Gungan Army acting as a distraction to the bulk of the main Trade Federation forces, the Naboo resistance led by herself, Captain Panaka and the Jedi will infiltrate Theed via a secret entrance located inside one of the waterfalls. Nute Gunray, hearing reports of the Grand Army's assembly, informs Darth Sidious; Sidious orders Gunray to wipe out both the Gungans and the Naboo as the Trade Federation prepares for battle.
Nagato comes out of Padme's ship he sneaks passed everyone makes his way to the hangar where the pilots are being held pulls out a communicator then tells Obi Wan to go with the gungans and Quigon with the queen and her people in order to win this battle they do as they are told which surpises everyone but Padme but she acts surpised so as to not raise alarm to herself once the other two jedi got to their postions and Anakin got into the cockpit with R2-D2 that's when everything went nuts and all hell broke loose Captain Roos Tarpals orders the Gungan Grand Army to activate their shield, which protects them from ranged attack. OOM-9 has his tanks fire first, but seeing them fail to penetrate the powerful shield, orders them to cease fire. Daultay Dofine gives the command to activate the battle droids These droids march through the shield and open fire on the Grand Army, Obi Wan does what he can but he's only one guy the droids soon destroy the shield generator. As the tanks cause heavy casualties among the Gungans, defeat for the alliance seems imminent.
However, victory comes when young Anakin Skywalker accidentally takes control of an N-1 starfighter and goes on to destroy the Federation's Droid Control Ship from the inside, killing Daultay Dofine and rendering the droid army useless. Meanwhile, Amidala and her force fight their way back into the royal palace and capture Nute Gunray
At the same time, in a Theed hangar bay, Darth Maul engages in combat with the Jedi, using his double-bladed lightsaber. The battle moves from the hangar, across a series of catwalks, to the Theed Generator Complex. During the fight, Maul is kicked off of a catwalk. He grabs the edge of another catwalk below and jumps back up to where Nagato is and continues to fight. By this time, Nagato and Maul have become separated by a force field in the entrance to the Generator Room. Obi-Wan and Quigon catches up to them, but is divided from their master by four force fields. When the force fields deactivate, Nagato and Maul continue their battle while Kenobi and Jinn remains divided from the battle by one force field when they all reactivate.
After a lengthy duel, Nagato suddenly stuns Maul by hitting him on the chin with his lightsaber handle, then rams his hilt straight into Maul's , face breaking his nose and his jaw humliated and angered, Maul redoubles his assault upon Nagato and chops the Jedi's cloak in half, but Nagato eventually overpowers and nearly kills Maul by Force pushing him over the edge of a seemingly bottomless reactor shaft. Maul saves himself from falling when he manages to grab onto a pipe protruding from the wall of the shaft. Nagato kicks the Jedi's lightsaber into the pit and prepares to finish him off. After Maul calms himself, he uses the Force to leap out of the shaft and over Nagato's head while summoning his fallen lightsaber to his hand He lands behind Nagato expecting to cut him in half but it was blocked and Maul's body was the one split in half Nagato uses the force to throw Maul's upper and lower body fall into the shaft.
The newly elected Chancellor Palpatine arrives to congratulate Queen Amidala on her victory, as Nute Gunray is sent to stand trial for his crimes later, in a room in the queen's palace, Yoda confers upon Kenobi and Qui-Gon regarding Anakin's training Yoda is convinced it is dangerous to train the boy, but tells Kenobi the Jedi Council has allowed Skywalker to become Kenobi's sparring partner but his master will be Nagato . Later that evening, in a temple in Theed, Mace Windu and Yoda agree that the Sith are definitely to blame for the bloodlust that they now sense in Naruto or as they know him Nagato As there are only ever two Sith at any given time (a Master and an apprentice), both Masters believe that one must still remain.
The Naboo and Gungans organize a great victory celebration on the streets of Theed, in front on the palace. Obi-Wan Kenobi and Anakin Skywalker are present, the younger now wearing formal Jedi attire, and in his hair is a special braid: the mark of a Jedi Padawan. Palpatine meets Anakin personally assuring the kid that he will be watching his career with 'great interest'. The festival ends with Queen Amidala presenting a gift of appreciation and friendship to Boss Nass and the Gungan people.