Dooku never asked to be a Sith Lord. He simply knew the Jedi as they existed were blindly following a Code that didn't line up with the times. Sidious offered him power, and he was seduced. But Dooku had never thought of himself as a true Sith. He didn't believe in the Sith creed of pure evil. While there were parts of Sith code that he believed were right, like the permission to form attachments, it for the most part was just as lost as the Jedi. So when Sidious approached him with his endgame, involving kidnapping the Chancellor of the Republic, Dooku realized the opportunity before him. The galaxy will never be the same. There are heroes on both sides.
"No loose wire jokes," said Anakin Skywalker, annoyed. His master's lack of faith in his trusty droid annoyed him. The two Jedi were in an elevator aboard a Separatist cruiser, on their way to rescue Chancellor Palpatine, who'd been kidnapped by General Grievous.
"Did I say anything?" Kenobi responded.
"He's trying."
"I didn't say anything!"
Suddenly, the speaker in the elevator activated.
"Artoo, was that you?" Anakin asked over his comlink.
"Jedi. We don't have much time," a familiar voice said over the speaker.
"Dooku," the two said.
"Palpatine and Darth Sidious are one in the same. He orchestrated the war from the beginning, playing both sides. If we play our cards right, we can stop him. Trust me. I cared for Qui-Gon just as much as both of you did."
Anakin and Obi-Wan looked at each other in a mixture of shock and confusion. They didn't have any more time to evaluate their options, as they'd arrived at their destination.
Palpatine was sure enough there, arms fastened to a chair. Cautiously, the Jedi approached.
"Chancellor," Obi-Wan carefully addressed, bowing.
"Count Dooku," Palpatine said, seeing the man approach from behind. Dooku strode out of a door onto a balcony. The three shared a look and Dooku jumped down.
"I think he's telling the truth," Obi-Wan whispered to Anakin.
"I was about to say that," he replied.
"Get help. You're no match for him, he's a Sith lord!" Palpatine said.
Obi-Wan took a deep breath. "Darth Sidious, Sith lords are our speciality." The Jedi spun around, backing up to let Dooku between them.
The rage that appeared over the Chancellor's face was unlike anything the Jedi had seen before.
"It seems you've caused the death of a mutual friend of ours," Dooku began. "One Qui-Gon Jinn. Now we have the dark lord of the Sith, strapped to a chair."
"I wish it were that easy for you," Sidious grinned. With the flick of his hand, the straps holding him to the chair released him. With one hand, he pulled Dooku's lightsaber to his hand, and with the other, threw Kenobi into a wall, knocking him out. Sidious threw himself at Dooku, but not before the Count pulled Kenobi's lightsaber to his hand. The Sith and his former apprentice engaged in a duel. As Sidious began to overpower Dooku, Anakin threw himself in between and began to give Sidious everything he had.
Sidious looked worried for a second, but grinned.
"You. Killed. Qui-Gon!" Anakin screamed. "You. Used. Me!"
"Yes! I did! And you were a fool! What are you going to do!"
"I'll kill you!" Anakin roared.
Sidious grinned widely. Anakin's eyes burned yellow as he overpowered the old Sith. Sidious was enjoying parrying the strikes of the young Force-wielder.
Anakin was feeling things he'd never felt before. The rage inside him boiled. The feelings of being used, the death of Qui-Gon, the death of his mother, the Jedi's treatment of Ahsoka. He had to stop Sidious here to see her again. Something rose up in him, and he raised his blade along with it. He brought it down, swinging hard and putting Sidious on the defensive. He took one hand off his blade, using the force to suspend Sidious' blade hand in the air as he drove his saber into the chest of the old man.
Sidious cackled as he fell to the ground, almost completely ignoring the pain as the boy who almost became his apprentice stood over him coldly. The Lord of the Sith dropped dead.
Anakin deactivated his saber and looked to Dooku. "What now?"
"The Sith are no more," Dooku replied.
Obi-Wan awoke with a start. "Anakin!" he yelled.
Anakin and Dooku ran over to him.
"What happened?" Kenobi asked.
"It's over, Master. I've ended the Sith," Anakin said.
"And so the prophecy has been fulfilled." Obi-Wan walked to Sidious's body, checking to make sure he was truly dead. He grabbed Dooku's lightsaber out of Sidious' cold hand and threw it to him. Dooku threw back Kenobi's saber to him.
Anakin, Dooku, and Obi-Wan headed for the command center of the ship, hoping to catch General Grievous. Knowing Grievous, Obi-Wan stayed by the escape pods while Anakin and Dooku charged into the command center. They cut through the droids, leaving only Grievous.
"General Grievous. You're shorter than I expected," Anakin said.
"Skywalker. I'd love to talk, but it looks like you don't have time," Grievous said, shutting down the engines of the ship. As Anakin and Dooku rushed to reactivate the ship, Grievous made his escape.
Unfortunately for the droid general, Kenobi was waiting for him.
"Hello there!" Kenobi said.
"General Kenobi! I hope to make your death painful."
"I'm sorry to crush your dreams, General."
Kenobi and Grievous locked sabers, but the duel was short-lived. Kenobi cut off Grievous' robotic hands, one at a time. Grievous tried to run but Obi-Wan held him in place with the Force. He plunged his saber into the General's heart. The three flew the ship back down to the surface of Coruscant.
They were met by Yoda and Mace Windu, along with Senators Amidala and Organa.
"Where is the Chancellor?" Organa asked.
"Why is Dooku with you?" Windu probed.
"I'll let Anakin take this one," Obi-Wan said.
"Chancellor Palpatine and Darth Sidious were one in the same. Dooku told us this shortly before we confronted him. I managed to kill him and Master Kenobi killed General Grievous shortly after."
"Disturbing, these revelations are. Glad, I am, that this conflict is over," Yoda said.
"Master Yoda, if I may," Dooku started.
"You may not. You may have helped us end the Sith, but you are still a traitor," said Windu.
"Talk, let him," Yoda said.
"The Sith may have been the Jedi's enemy, but you've allowed them to grow without you knowing. The Jedi have been corrupted by their misinterpretation of texts. The Jedi were founded on the basis of balance. The light and the dark, letting neither side take priority over another. The light side promotes compassion, but at the cost of attachment and passion. The dark offers power and passion at the cost of compassion. To find a balance is the goal of a Jedi. Anakin Skywalker has done this. This is why he was able to end the Sith and why he is the Chosen One."
Yoda pondered Dooku's statement. "See now, I do. Blind, we were. Anakin Skywalker, grant you the rank of Jedi Master we do, for your mastery of balance. Grateful, the galaxy is."
Anakin bowed. "Thank you, Master."
Just as Anakin stood, a Venator-class ship landed. Out stepped Ahsoka Tano, followed by Commander Rex, Captain Vaughn, ARC Trooper Jesse, and the 332nd company.
"Maul was able to escape," Ahsoka said. "We captured Saxon and the rogue Mandalorians, but it was almost like he sensed something, I did too."
Anakin smiled at her. Ahsoka realized what the smile meant. She ran up to Anakin and hugged him. "Is it over?" she asked her former master.
"It is, Snips, it's finally over."
"Y'know," Jesse said, elbowing Rex, "I wasn't sure we were gonna make it out alive, for a bit there." He laughed.
"Speak for yourself," replied Vaughn.
The clones laughed as more joined them to welcome them back. Cody, Gree, Grey, Hunter, Crosshair, Wrecker, Tech, and Echo all cheered for the end of the war.
Padmé Amidala ran up to Anakin. "Ani, I have wonderful news."
"What's that m'lady?" Anakin replied.
"I'm pregnant."
Anakin Skywalker went public with his marriage to Padmé Skywalker. Padmé safely birthed twins, Luke and Leia Skywalker, who both went on to become powerful Jedi. Padmé succeeded Palpatine as Chancellor of the Republic, restoring it to the glory it once had. Anakin eventually succeeded Yoda as the Grand Master of the Jedi, teaching a balance of the light and dark sides of the Force.
Ahsoka Tano rejoined the new and improved Jedi Order. She was immediately promoted to the rank of Knight and took an apprentice after her promotion to the rank of Master.
Obi-Wan Kenobi tracked down Maul after a few years of searching, finishing the fight he started on Naboo and ending Maul's criminal empire. He became one of the most revered Jedi Masters in the history of the Jedi Order.
Dooku rejoined the Jedi Order as well, specializing as a lightsaber combat instructor.
Clone Commander CT-7567, or Rex, ascended to the highest rank in the clone army, along with CC-2224, or Cody. The two were the military leaders of the Republic, continuing to work with the Jedi Order. The clone army were allowed to lead their own lives, or continue to serve to protect the Republic if they desired. Rex's investigation into inhibitor chips led to the discovery of their purpose, and all clones removed their chips.
Clone Force 99 served as leaders in the New Republic military, and met a young female clone known as Omega, who they gladly accepted into their ranks, as she was different, like them. The five original members were like parents to her, until she reached adulthood and joined them in the military.
The Kaminoans stopped cloning, letting a final batch of clones be created, free to choose whatever path in life they wanted.
Luke Skywalker was trained by his father, reaching the same level of power and mastery of the Force. Luke succeeded his father as Grand Master of the Jedi Order. Luke met a woman named Mara Jade, and had one son, Cade.
Leia Skywalker was trained by Master Ahsoka Tano. She was known for her strength and compassion and became a Jedi legend like the rest of her family. On one mission, she met a young man named Han Solo, who joined the Republic Military as a naval officer and starship captain. The two eventually married and had one son, Ben Solo.
Cade Skywalker and Ben Solo were both inducted into the Jedi Order, and some of the most powerful Jedi in history. Solo was especially remembered for his similarities to his grandfather, Anakin Skywalker.
Master Yoda passed away twenty-three years after the end of the Clone Wars, leaving behind a legacy as one of the most pure-hearted and kind Jedi Masters.
Mace Windu gladly offered Anakin Skywalker the position of Grand Master, and served as Skywalker's advisor. He died as the last great Jedi of his era, before the revamp of the Order.
The ghost of Qui-Gon Jinn discovered how to create his human form, and taught all Jedi how to preserve life after death. This meant that once a Jedi died, they were able to stay in the Temple to give their knowledge to help the next generation protect the galaxy.
The Republic prospered under Chancellor Padmé Skywalker. The Sith never returned, thanks to the leadership of Grand Masters Anakin and Luke Skywalker. The Jedi had saved the galaxy and found balance.
