The Galaxy has spent 1000 years at peace. The Jedi order is dedicated to keeping that peace, dealing with any conflicts that arise across the galaxy. The planets in the known galaxy are organized into a Galactic Republic, a democratic government run by the Galactic Senate and one Supreme Chancellor.
Jedi Master Dooku, an old apprentice of Grand Master Yoda, becomes disillusioned with the Republic after going on several missions with his own apprentice, Qui-Gon Jinn. He peacefully leaves the Jedi order, but is allowed to keep his lightsaber and to reenter the Jedi Temple as he pleases. He is approached by Sheev Palpatine, a Republic Senator who is secretly a dark lord of the Sith called Darth Sidious. Palpatine offers Dooku the power to continue his fight against corruption in the Republic through the dark side of the force, and Dooku agrees.
Jedi Master Sifo-Dyas has a vision of Galactic War and attempts to warn the Jedi, which leads to him being removed from the Jedi Council and being declared a warmonger. He then takes it upon himself to commission an army for the Republic from the cloners on Kamino. This attracts the attention of Palpatine, who keeps an eye on Sifo-Dyas from the shadows.
Sidious orchestrates an invasion on the planet Naboo through a group called the Trade Federation. Qui-Gon Jinn and his Padawan Obi-wan Kenobi are sent to end the dispute. They rescue the queen of Naboo, Queen Padmé Amidala, but are forced to hide out on a nearby Planet, Tatooine. There, they meet a young slave boy named Anakin Skywalker. Qui-Gon believes Anakin to be the chose one mentioned in Jedi Prophecy, so he arranges for his freedom. However, he is not able to free his mother, so Anakin leaves her behind to become a Jedi. They take Anakin back to Coruscant, the capital planet of the Republic, and the location of the Jedi Temple. There he is to be trained by Qui-Gon.
Once there, Queen Amidala calls for a vote of no confidence in the current Chancellor, blaming him for the republics failure to help her homeworld. This results in Senator Palpatine to be voted into office as new chancellor of the Republic. While this is happening, While this is happening, Count Dooku visits the Jedi temple and erases Kamino from the Jedi archives to prevent anyone from finding out about the clone army being created.
Qui-Gon, Obi-wan, and Queen Amidala return to Naboo to remove the blockade by force. With the combined force of the Naboo Army and the Gungans, a race of Aquatic people who lived in the oceans of Naboo, they were able to defeat the Trade Federation and their droid army.
While this is happening, Qui-Gon and Obi-wan are confronted by Darth Maul, the apprentice of Sidious. Maul fatally wounds Qui-Gon, but is ultimately cut in half by Obi-wan. Kenobi watches his master die in his arms, and promises to take on Anakin as a Padawan in Qui-Gons place.
Dooku mourns the death of his former Padawan, which ultimately pushes him father into the dark side of the force. He arranges for the death of his old friend Sifo-Dyas. He then takes control of the development of the clone army, having inhibitor chips put in their heads. He recruits Jango Fett, the most feared bounty hunter in the galaxy, to become the genetic template for the clones. Fett requests to have an unaltered clone for himself to raise as his son along with his financial compensation. He names his son Boba, and intends for him to carry on his legacy.
Ten years after the Battle of Naboo, Count Dooku founds the Confederacy of Independent Systems, leading to thousands of systems seceding from the Republic. This causes the Republic Senate to debate about the creation of an army. Many senators, including Padme, the queen turned senator of Naboo, oppose this action.
Sidious instructs Dooku to assassinate Padmé. Dooku sends Jango Fett, who sends a different bounty hunter names Zam Wesell, who sends her droid, who sends some bugs to kill Padmé. This assassination attempt was thwarted by Obi-wan and Anakin, who had been assigned as Padmé's protectors. Obi-wan begins to investigate the assassination attempt, leaving Anakin to protect her on his own.
Anakin and Padmé travel to Naboo, thinking it would be a safer place to lay low. However, once there Anakin begins having visions of his mother’s death, so he and Padme decide to go to Tatooine to try and rescue her.
Once there, they discover that she had been freed and found where she was last known to be; the Lars homestead. There they met Cleeg Lars, as well as his son Owen and Owen’s girlfriend Beru. Cleeg informs Anakin that she had been taken by Tuskin Raiders. Anakin is able to hunt down the Tuskin Raiders camp and finds his mother, who dies in his arms. This causes Anakin to go on a rampage, killing the entire camp. Not just the men, but the women and the children too. Somehow Padmé doesn't see this as a red flag.
On the other side of the galaxy, Obi-Wans investigation leads him to Kamino, where he discovers the practically finished clone army, as well as Jango Fett. He confronts Jango, who flees to Geonosis, where the leaders of the separatist alliance were currently meeting, Dooku included. Kenobi follows Jango there, but is discovered and captured, but not before sending a message to Anakin and the Jedi Council.
Fearing the growing numbers of the separatists, the senate grants Palpatine emergency powers, which he uses to override the vote on the Military Creation Act, and approves the use of the clones as their military force.
Anakin and Padmé travel to Geonisis to rescue Kenobi, but are captured as well. The three of them are then sent to the Geonosian Arena, where they are to be killed for entertainment. Thankfully, all available Jedi arrive to save them, as well as Master Yoda with the clone army. At this battle, Dooku reveals himself as a Sith, and duals Obi-Wan, Anakin, and Yoda, taking Anakin’s arm. At the same time, Mace Windu kills Jango Fett in front of his son. At the end of this affair, Padmé and Anakin, who had been developing a relationship throughout their time together, decide to get married in secrete.
The battle of Geonosis begins the three year war known as the Clone Wars. The Grand Army of the Republic, made up of Clones led by the Jedi Order, fights against the forces of the Separatist Alliance, made up of their droid army. Due to the ongoing conflict, many Jedi Apprentices are promoted to Knights to help fill leadership roles and lead clone legions. Anakin leads the 501st with the help from Clone Captain rex. During a mission on Christophsis, Anakin is sent his own assigned Padawan, Ahsoka Tano.
Fearing that the planet Mandalore will join the Separatist Alliance, the Jedi send Obi-Wan to meet with the Duchess of Mandalore, Satine Kryze, a person who he had been sent to protect in the past and had formed a romantic relationship with, but ultimately left behind to attend to his duties as a Jedi. She is currently being targeted by Death Watch, a group that intends to revert Mandalore back to its more traditional ways of violence.
Maul, who survived being cut in half by Obi-Wan all those years ago, returns. He allies himself with Death Watch, and they successfully capture Satine, placing Mandalore under their control. Maul kills the leader of Death Watch, claiming the throne of Mandalore for himself.
Bo-Katan, member of Death Watch and sister to Satine, denies the leadership of Maul, and sends a message to Obi-Wan asking for his help. He attempts to rescue Satine, but is instead captured and forced to watch Maul fatally wound Satine. She dies in his arms. Bo-Katan helps Obi-Wan escape.
Ahsoka is framed for an attack on the Jedi Temple and sent to trial. She is proven innocent, however this event causes her to turn her back on the Jedi Order. This, as well as other events during the clone wars, shakes Anakin’s trust in the Jedi council.
Bo-Katan finds Ahsoka Tano on Coruscant and asks for her help removing Maul from power. She goes to ask help from Obi-Wan and Anakin, who sends a battalion from the 501st legion, including Captain Rex, to help her. They are sent to Coruscant to fend off a separatist attempt to kidnap Palpatine. Anakin and Obi-wan stop the kidnapping attempt, Anakin killing Count Dooku in the process.
Ahsoka duels Maul and successfully captures him. Mandalore falls under Republic occupation as Maul is transported to Coruscant to be imprisoned for his crimes against the Republic.
Obi-Wan hunts down General Grievous, the leader of the droid army. He finds him on the planet Utapau. Obi-wan defeats him, leaving the Separatists with no leaders.
Padmé reveals to Anakin that she is pregnant, and he begins to have visions of her death. Desperate to save his wife, he turns to his good friend Chancellor Palpatine, who reveals himself to be a Sith Lord, offering to help Anakin save his wife if he joins him.
Anakin at first reports this discovery to Jedi Master Mace Windu, but when Windu goes to end the Sith once and for all, Anakin steps in and stops him, resulting in the death of Mace. Anakin then joins Darth Sidious in the interest of saving his wife and unborn child, taking on the title Darth Vader.
At this point, Darth Sidious enacts his master plan that he had set in motion all the way back when Dooku took over the production of the clones. He had a chip implanted on the clones brains that, when activated, would cause the clones to turn on their Jedi and kill them. This would cause the death of 90% of the Jedi order. Anakin lead the 501st on a march on the Jedi temple with the goal of wiping out all the Jedi that remained in its halls.
Ahsoka’s clones turn on her while she is transporting Maul back to the Republic, which results in Maul escaping and the death of all the clones on the cruiser, except for Rex, who Ahsoka was able to remove the inhibitor chip from. Ahsoka and Rex escape and go into hiding.
Obi-Wan and Yoda escape their clones and return to Coruscant, where they discover Anakin has turned to the dark side and Palpatine was the Sith Lord they were looking for. Obi-Wan goes to confront Anakin while Master Yoda goes to confront Palpatine.
Obi-Wan stows away on Padmé's ship when she goes to see him on Mustafar. Anakin, thinking that Padmé brought Obi-Wan with the purpose of killing him, turns on his wife and attacks her, leaving her unconsious. Anakin and Obi-Wan then duel, leaving Anakin dismembered and horribly burned, but still alive.
Yoda confronts Palplatine in his office. He tries to end the rule of the Emperor before it begins, but is defeated and goes into exile on Dagobah.
Obi-wan takes Padmé to a nearby hospital, where she dies giving birth to twins she names Luke and Leia.
Luke is sent to his Uncle and Aunt on Tatooine, and Leia is sent to Padmés dear friend Bail Organa and his wife on Alderaan. Obi-wan goes into exile on Tatooine to watch over Luke, and eventually train him to be a Jedi.
Sidious finds Vader horribly disformed on Mustafar and brings him back to Coruscant where he is placed in a metal suit to keep him alive. He is told that in his anger, he caused the death of his wife and unborn child. Sidious tells the people of the Republic that the Jedi had turned on them and attacked him, but were ultimately defeated. He also announces that the Clone Wars had ended and that the Republic would be reorganized into the first galactic Empire.