The Phantom Menace Extended Edition 3

The film begins with a narrator explaining the state of the Clone Wars instead of an opening crawl, like its predecessors. The Separatists control the majority of the hyperlanes, leaving Republic forces stranded in different parts of the Outer Rim. Jabba the Hutt's son Rotta is kidnapped as part of a plan to make the Hutts join the Separatists. Meanwhile, a fierce battle is taking place on the crystalline planet of Christophsis between the Republic's very limited clone army and the Retail Clan forces.

With the help of Obi-Wan Kenobi and Anakin Skywalker, the clones steadily advance on the Separatists' forces, gaining the Republic an early victory. It doesn't last long, though, as the droid army soon returns. With no communications or the ability to fly in reinforcements, the fate of the few remaining clone soldiers are in the hands of Obi-Wan and Anakin. A shuttle arrives, but without the needed reinforcements—instead, it is a young Padawan named Ahsoka Tano, who insists that she has been sent by Master Yoda to serve under Anakin. The battle soon commences yet again, with the Separatist forces advancing behind an expanding shield that artillery can't penetrate. Anakin and Ahsoka succeed in penetrating the enemy lines while Obi-Wan stalls for time by holding a fake surrender negotiation with the droid army commander.

Soon after the final victory for the Republic on Christophsis, Yoda arrives and brings the Jedi up to date on the situation concerning Jabba's son. The Republic needs Jabba on their side to ensure unfettered travel through Jabba's trade routes. Anakin and Ahsoka are tasked with retrieving the child, while Obi-Wan flies to Tatooine to assure Jabba that Rotta will be retrieved.

On the planet Teth, Anakin, Ahsoka and their clones assault a monastery that sits atop a high stone pillar. They find Rotta, but discover that he is ill, requiring them to get him help immediately. But they have been caught in a trap by Count Dooku, who hopes to frame the Jedi for Rotta's disappearance (and possible death), thereby ending any chance of the Republic striking a deal with Jabba. He has sent his minion, Asajj Ventress, to secure fake evidence of the Jedi's supposed double dealing, then to recapture the young Hutt and return it to Jabba, putting the crime lord in the Separatists' debt.

Anakin and Ahsoka manage to escape the trap along with R2-D2 and hijack a derelict transport which they use to travel to Tatooine. Obi-Wan, alerted by Anakin, arrives just in time to relieve the clone forces and engages Ventress in a lightsaber duel where he manages to defeat her, though Ventress flees in the face of capture. On board the derelict ship, Ahsoka manages to cure Rotta by the use of medical supplies on board.

In the meantime, Senator Padmé Amidala learns of Anakin's mission and fears for his safety. She decides to contact Jabba's uncle, Ziro, who lives in a shady part of Coruscant. The Hutt refuses to cooperate, apparently believing that it is the Jedi who are responsible for the situation. Padmé, however, soon discovers that Ziro has actually conspired with Dooku to engineer the downfall of his nephew in order to seize power over the Hutt clans. Padmé is discovered and detained, but a chance call by C-3PO enables her to summon help, and Ziro is arrested.

Upon their arrival on Tatooine, Anakin and Ahsoka are attacked and shot down. Faced with a long trek across desert sands and relentless opponents, Anakin devises a ruse: he confronts Dooku while carrying a decoy Rotta, leaving Ahsoka and R2-D2 to take the real Rotta to Jabba's palace. While Anakin fights Dooku, Ahsoka is ambushed by three Magnaguards, whom she narrowly defeats. Anakin and Ahsoka enter the palace one after another and Rotta is returned to his father. Jabba, deceived by the lies of Count Dooku, orders for them to be executed. Just in time, Padmé calls and convinces Jabba of his uncle's duplicity. Jabba agrees to allow the Republic safe passage through the Outer Rim territories, but only if the Jedi promise to make Dooku pay for his crimes against the Hutts. With their mission accomplished, Anakin and Ahsoka are triumphantly retrieved by Obi-Wan and Yoda.

The opening crawl reveals that the Trade Federation has blockaded the planet of Naboo in hope of resolving a galactic trade dispute. Chancellor Valorum of the Galactic Republic secretly sends two Jedi Knights — Qui-Gon Jinn and his padawan learner Obi-Wan Kenobi — to meet with the Trade Federation to settle the crisis. Unknown to them, the Trade Federation is in league with the mysterious Sith Lord Darth Sidious, who orders them to invade Naboo with their immense droid army as well as kill the two Jedi. Qui-Gon and Obi-Wan escape and flee to the surface of Naboo, where they meet local Gungan outcast Jar Jar Binks. As Jar Jar brings them to an underwater Gungan settlement, the Trade Federation captures Naboo's leader, Queen Amidala. Through a Jedi mind trick, Qui-Gon secures a submarine, which he, Obi-Wan, and Jar Jar use to reach the capital of Naboo and rescue Queen Amidala and her escort. The group departs for Coruscant, the Galactic Republic's capital planet, to seek help from the Senate.

During the escape, the ship is attacked by the Federation blockade, forcing R2-D2, one of the ship's droids, to fix the shields. The attack damages the ship's hyperdrive, forcing the party to land on the desert planet of Tatooine for repairs. While searching for needed parts, Qui-Gon and a handmaiden named Padmé befriend young Anakin Skywalker, a nine-year-old human slave gifted in piloting and mechanics. Qui-Gon senses a strong presence of the Force in Anakin, and feels that he may be the "Chosen One" — an individual the Jedi believe will fulfill a prophecy by bringing balance to the Force. At Anakin's insistence, Qui-Gon enters Anakin into the Boonta Eve Podrace in a bet with Anakin's master, Watto, to gain the needed parts as well as Anakin's freedom. Anakin eludes several obstacles—including rival racer Sebulba—to win the race, gaining his freedom and bankrupting Watto. After hesitation, Anakin leaves his mother and his droid (C-3PO) behind on Tatooine to go with the Jedi. As the group prepares to depart, they are attacked by the Sith apprentice Darth Maul, who battles Qui-Gon until the heroes escape. On Coruscant, Qui-Gon informs the Jedi Council of the mysterious, well-trained attacker. The Council becomes concerned that this may indicate the reappearance of the Sith, an opposing order that followed the dark side of the Force. Qui-Gon informs the Council about Anakin, hoping that he can be trained as a Jedi. After testing the boy the Council refuses, worried that he is too old for training and that the fear and anger that he harbors will cloud his future. Meanwhile, Senator Palpatine of Naboo persuades Amidala to call a vote of no confidence in Chancellor Valorum. The vote removes Valorum from power and leads to Palpatine's nomination for the position, which Amidala considers too late to be effective. To stop the Federation invasion by herself, the Queen decides to return to Naboo with her security team, the two Jedi, R2-D2, Anakin, and Jar Jar.

On Naboo, Padmé reveals herself as Queen Amidala and forms an alliance with the Gungans for the battle against the Trade Federation. The Gungans march into battle to divert the Federation army away from the capital, allowing the others to infiltrate the palace. Once inside the palace hangar, the Jedi free several Naboo pilots, who regain their starfighters and assault the Federation droid ship. As they make their way to the throne room, the infiltration team is confronted by Darth Maul. Qui-Gon and Obi-Wan engage Maul while the others take an alternative route. Qui-Gon and Obi-Wan duel with the Sith Lord amongst the catwalks of a massive power-generating reactor core. Obi-Wan is briefly delayed, separating him from Qui-Gon and Maul. Meanwhile, Queen Amidala and her forces fight their way into the palace and capture Nute Gunray, Viceroy of the Trade Federation. Anakin—inadvertently joining the dogfight in space—destroys the droid-control ship's reactor with proton torpedoes, which deactivates the droid army in the midst of taking Gungan prisoners. In the reactor core, Qui-Gon re-engages Darth Maul singlehandedly, but is mortally wounded. Obi-Wan catches up with and defeats Maul in another intense lightsaber battle. With his final breath, Qui-Gon instructs Obi-Wan to train Anakin to become a Jedi.

In the aftermath, the newly elected Chancellor Palpatine congratulates Queen Amidala on her victory and promises to watch Anakin's career with great interest. Meanwhile, the Jedi Council promotes Obi-Wan to the level of Jedi Knight, and Yoda reluctantly accepts Obi-Wan's request to train Anakin as his padawan. During Qui-Gon's funeral, Mace Windu and Yoda agree that Maul was indeed a Sith. However, because there are always two Sith at any given time (a master and an apprentice), they believe that another Sith still exists, although who that Sith is remains uncertain. A large celebration is held on Naboo to celebrate the world's liberation and the newborn alliance between the Naboo and the Gungans.