Star Wars: Episode III

Revenge of the Sith

AU

AN: My exams are OVER! To celebrate, I proudly present my version of Star Wars Alternate Universe! I took inspiration from Star Wars: The Clone Rebellion fanfic as well as various other 'Defying Order 66' stories. This, however, is my view of what if. This will span towards the Return of the Jedi as well as the upcoming Force Awakens. The original story, will of course change due to the events that will come up here in this story. But in this episode, it is the beginning!

I don't own Star Wars or any other related stuff. This is my own story, using the characters in the Star Wars Universe. NO FLAMES ALLOWED!

Episode III: Beginning of the Clone Rebellion

Sidious appears at last! He orders turned sith, Anakin Skywalker to take the 501st Legion to annihilate the Jedi Order. At the same time, orders all Clone commanders to execute order 66. This is the story of how the Grand Army of the Republic responds to the order!

Utapau

Commander Cody, of the 212th Attack Battalion, received a holo message from the Chancellor to execute Order 66. However, unknown to Sidious, the order was discovered by Commander Neyo at the beginning of the Clone Wars. Having found out about the biochip, Neyo had ordered the Kaminoans to remove them, thereby rendering the clones affected free of brainwash. However, only a few parts of the Grand Army of the Republic were free of the biochip's influence.

'The Chancellor thinks he could fool us. Heh….we had him fooled all along,' thought Cody as he pocketed his holo-transmitter.

Unknown to him, there was a lone Coruscant Security Guard in the rocks, watching every movements the Clone commander made. Having saw him disobey the order, he readied his DC-15X sniper rifle to take out the commander. Whilst he was getting prepared, a 212th clone, by the name of Boil, snuck up on the security guard and shot him with a stun shot from his DC-15S carbine. Boil then dragged the guard to Cody.

Cody saw Boil and wondered what was going on. Going up to said clone, he asked, "Boil, what are you doing?"

"Sir, I saw a Coruscant Guard about to take a potshot at you and deduced that he was there to watch your movements and to take out General Kenobi," Boil replied.

Cody then realised that even if the Clone commanders disobeyed the order, many of the lone snipers like the one they've encountered would follow the order.

"Contact the rest of the commanders and tell them to watch out for clones in red. We are going to have our hands full soon," said Cody as he contacted Obi-Wan

"General, we have a problem. Order 66 is being carried out, but the 212th Attack Battalion will stand by your side. We need to leave now in order to regroup with the rest of GAR," said Cody.

Obi-Wan heard the message and replied, "Alright, Cody. But you're going to have to explain what Order 66 means when we get to the Negotiator."

Coruscant

Meanwhile, Anakin Skywalker walked towards the 501st Legion's barracks, and when he entered, he found many of the Clones aiming their DC-15A rifle and DC-15S carbines at him.

'What?! What's going on?! Do they know?!' thought Anakin as he began to ask himself millions of questions in his head, until Commander Appo walked in front of him with a blaster carbine in his hand.

"General Skywalker, you're being relieved of duty and you are under arrest for treasons against the Republic," stated Appo with a heavy heart

"What is the meaning of this, Appo?! Have you gone mad," shouted Skywalker as rage took over him.

"Actually, Sir, I am sane. We heard what had happened in the Chancellor's office from Commander Thire. We rebel because it isn't right to murder those who have protected the Republic more than we have. Therefore, you're being relieved of duty. I'm sorry," explained Appo as he signalled the men to surround the former Jedi.

"Surrender General. We have you outnumbered," pleaded Appo for the last time.

Anakin then force pushed his former soldiers and ran as the 501st fired their blasters on him. As he escaped, many more of the 501st came towards him in an effort to stop him but they were easily killed by Anakin's lightsaber. He got in a BARC speeder and took off. Appo and his men continued to fire until Anakin was well out of sight.

Having seen Anakin escape, Appo ordered the men to pack up everything and head to their fleet to escape the city planet. As the men took off to prepare, he got on his comm and said, "Commander Thire, we failed to stop Anakin. I lost a few of my men, but General Skywalker escaped."

In his barracks along with Rhys, Jeck and around 50 other Coruscant security guards, Thire heard the report and replied, "Alright Appo. We're going to regroup with you and come along. My men have taken a few padawans from the temple, but we were unable to convince the rest of the jedi to escape. See you soon. Thire out."

Appo bowed his head in sadness as he heard of the jedi that left behind to protect the temple. ARC trooper Fives went up to Appo and said, "The men are ready in the Venators and waiting your orders, sir."

Appo took a moment to look at the jedi temple and saw smoke rising from it. "heh…must have been the Coruscant Guard that have taken the job that we were supposed to do. Traitors to the true Republic.'

"Alright Fives. Let's go," said Appo as he put his helmet on.

Narrator: Many Jedi master fell to sniper shots from the Coruscant Guards, leaving their clone commanders to regroup with the rest of GAR. However, the saved jedi included Obi-Wan Kenobi, Plo Koon, Ahsoka Tano and Grand Master Yoda.

Naboo System, Kaliida Shoals Medical Center

Many of GAR's fleets of Venators regrouped at the medical center. Out of all the Army, 212th Attack Battalion, 327th Sky Corps, 21st Nova Corps, 104th Battalion, 91st Mobile Reconnaissance Corps and the 501st Legion were those that had made their journey to the medical center. Many of others were loyal to the Chancellor, but some of the clones were also making their way to the medical center. All the clone commanders met with the surviving jedi, as well as Senator Bail Organa, and formed a meeting to decide the next course of action.

The clone commanders sat around the holo table with the jedi at opposite ends. Appo opened the meeting and said, "The 501st Legion with some 50 of Coruscant Guards commanded by Thire escaped Coruscant. We managed to save a few padawans, but the rest stayed behind to defend the temple," Appo explained what order 66 was to those who hadn't heard of it, and it left the jedi and Bail in shock that such an order was created.

Following Appo's example, other clone commanders gave their report on the situation and some clone commanders were left without their jedi counterpart, as they had been assassinated by the Coruscant Guards.

Neyo was the final clone commander who gave a debrief. "My boys on Coruscant tell me of a signal coming from the temple that tells all jedi to return."

Obi-Wan then spoke, "Well then, it is clear that this is a trap. Master Yoda, we should go back. We need to change the signal to warn all jedi to stay away from Coruscant."

Yoda agreed and said, "Agree with you, I do. Thire, get Rhys and Jeck to come along. Useful, you three shall be."

"Yes Sir, I shall get them ready," replied Thire as he went out of the room to prepare for the mission.

The meeting was concluded, with many of the clone commanders agreeing to go to Kamino to evacuate the many Kaminoans that were loyal to the true Republic, as well as to the Jedi. Whilst walking back to the 501st Legion, Appo was stopped by Cody.

"Yes, Cody?" asked Appo.

"You didn't tell them about Skywalker?" asked Cody, who was curious about the missing details. Many of the Clone commanders were briefed upon by Appo before the initial meeting, and many of them were shocked as well as sad that the most respected jedi had turned sith.

"I do think General Kenobi needs to learn the truth, but General Yoda confronted me about this already. I think he sensed my distress. He then ordered me not to reveal this to Commander Tano and General Kenobi. I just hope he made the right decision." Said Appo as he looked at the empty hall with a sad face

"So do I, Appo. So do I," replied Cody.

As the clone commanders left with their respective fleet to Kamino. Obi-Wan and Yoda headed to Coruscant in Organa's ship along with Thire, Jeck and Rhys to the Jedi Temple.

Coruscant, Jedi Temple

The temple entrance was guarded by the Coruscant Guards, and many of them tried to shoot the two jedi, but were easily cut down by their lightsabers. Most of the guards that were coming out of the temple were shot down by Thire and his men. When the group came in, they were greeted with the sight of a massacre. Clone bodies everywhere, along with the jedi and padawans.

"Not even the younglings that were hiding survived," said Obi-Wan

"Killed not by clones this Padawan. By a lightsaber, he was," said Yoda as he looked on in sadness.

Obi Wan bent down to inspect the body and saw a single hole through the it. Analysing it, it evident that this was a lightsaber scorch mark. He turned to Yoda and said, "…Who? Who could have done this?"

They ventured further down, while Thire and Rhys picked up the holocrons. Jeck followed by planting hidden sensors to warn them any approaching guards. The group made their way to the signalling chamber, they easily changed the transmission code.

When the code changed, they ventured into the security room when Kenobi said, "Wait, Master. There is something I must know." He walked towards the security recordings and flipped through the holo videos.

"If into the security recordings you go, only pain you will find." Warned Yoda

"He's right sir. You don't want to know," said Thire as he removed his helmet.

"I must know the truth," replied Obi-Wan

What he saw shocked and horrified to see Anakin slaughtering the jedi with ease. Yoda bowed his head in sadness while Thire closed his eyes, unable to watch the massacre.

"It can't be….it can't be," said Obi-Wan as he refused to believe what he was seeing.

After Darth Sidious congratulated his new apprentice in the holo video, Obi-Wan turned the video off, unable to watch any further.

"Destroy the Sith, we must," said Yoda

Obi-Wan, unable to face his old apprentice, begged Yoda to allow him to confront the Emperor instead.

Yoda refused and said, "Twisted by the dark side, young Skywalker has become. The boy you trained, gone he is . . . Consumed by Darth Vader."

Obi-Wan heavily sighed and nodded. "I do not know where the Emperor has sent him. I don't know where to look."

Yoda replied, "Use your feelings, Obi-Wan, and find him, you will. Visit the new Emperor, my task is. Thire, get more men, you should. A LAAT/I, needed it will be, should my mission fail."

"Yes, sir," replied Thire as he issued the orders to Rhys and Jeck

"Command the 501st and your battalion, Obi Wan. Useful, they are. In capturing Darth Vader. May the Force be with you," said Yoda.

"May the Force be with you too, Master," replied Obi-Wan as he watched Yoda and the clones depart the temple.

Kamino, Tipoca City

In the capital city, chaos ensued. Many rogue clones, led by Plo Koon and Ahsoka Tano, took many rogue Kaminoan scientists and armoursmiths, cloning equipments, building materials and droids as well as rogue Kamino Security teams to their ship and off the facilities. Whilst doing so, they battled the loyal to the Empire security team. Many of the security guards were lost, but were being replaced faster than they were being killed. The rogue forces managed to extract their mission objectives and scrambled out of Kamino before the security team could strike a blow. The rogue forces lost some clones in the process, but their skills saved them from dealing with heavy casualties on their side.

Naboo System, Kaliida Shoals Medical Center

The 501st, 212th and the 327th Sky Corps stayed at the facility to defend it from the Empire's navy. Appo and Cody talked about setting up hidden bases, particularly on Tatooine and Yavin IV, until Obi-Wan contacted them.

"General, what can we do, sir?" asked Appo

"I need both the 501st and the 212th to go to Mustafar. It seems Anakin is there. My orders are we stop Anakin or if things go south, kill him," said Obi-Wan.

Appo replied with a heavy sigh, "Yes sir. We will move out straight away."

Appo put his helmet on and faced Cody, "Well, this is it. Our chance to stop the Empire."

Cody nodded and put on his helmet. The 501st and 212th immediately took off to Mustafar. Within minutes, they arrived at said planet, and both rogue forces sent 5 LAAT/I, each with 5 clones, to the surface, while 5 more waited in the Venators as backup.

Mustafar

The LAAT/Is arrived and the clones exited the transport to support Obi-Wan. The clones were led by Captain Rex and Commander Cody for the mission, Appo stayed behind, stating that he didn't want to face the fallen jedi for a second time. The clones arrived, and saw Obi-Wan kneeling over Senator Padme Amidala. Rex quickly ordered the team medic, Kix, to take care of the Senator as the clones began to surround the former jedi.

"Sir, you're under arrest. Please don't make this any difficult for the men," said Rex as he pulled out his blaster pistols.

"YOU HAVE ALL BETRAYED ME!" shouted Anakin as the clones circled around him.

"You have done that to yourself," replied Obi-Wan as he faced Anakin and discarded his cloak.

"You are a traitor, sir. Killing younglings isn't the right thing to do. You know that," said Rex as he levelled his blaster pistol at Anakin

"Don't lecture me! I see through the lies of the Jedi! I do not fear the dark side as you do! I have brought peace, justice, freedom, and security to my new Empire," said Anakin darkly.

"New Empire?! Our allegiance is to the Republic…to the true democracy. The Empire is corrupt! Please, sir! Don't make us do this," pleaded Rex.

"If you're not with me, you're my enemies," said Anakin as he unhooked his lightsaber.

"Only a Sith Lord deals in absolutes. I will do what I must," said Obi-Wan as he too ignited his lightsaber.

"You will try," said Anakin as he ignited his lightsaber.

"Get him, boys," shouted Rex as he fired his pistols.

The other clones started firing, but Anakin deflected the lasers and managed to slice 10 clones, as they had gotten too close to his lightsaber. Before he could kill Cody, who was also near Anakin, Obi-Wan intervened and blocked the lightsaber.

"General," shouted Cody as he got up.

"Cody, leave some of the men to protect Senator Amidala. I want you and Rex to lead several clones with me," shouted Obi-Wan as he fiercely duelled with Anakin.

"Yes, sir," shouted Cody as he relayed the order and gave chase to the two duelling jedi.

Coruscant, LAAT/I

Thire managed to find fellow Commander Stone and his squad of 3. Jeck was the pilot of the ship, and contacted Yoda, who ordered, "Hurry. Careful timing we will need."

"There aren't many guards on this side. Activate your homing beacon when you're ready, sir," said Jeck.

"Commander, we will be receiving the General soon," said Jeck

"Copy that," replied Thire.

Yoda managed to make his way to the rendezvous point and a lone LAAT/I appeared. The former Grand Jedi Master jumped and made his way through the side doors. When he got in, the side doors closed and they all headed towards the atmosphere.

"Into exile I must go. Failed, I have," said Yoda to Thire as he sat down.

Mustafar

The duel carried on, and the clones tried to take a shot, but couldn't as they were worried that they might shoot Obi-Wan. They managed to get into the room, where they were greeted with the sight of dead Separatist leaders. When Anakin held Obi-Wan's lightsaber hand and began to choke the Jedi master, the clones began to fire at Anakin. The sith let go of his old master to deflect the lasers back at the clones. Two clones were hit by their lasers and went down. The three other troopers carried the two back to the cruisers, while Rex and Cody decided to stay behind to help Obi-Wan. The duel continued all the way up to a stream of lava. Both clone officers were unable to get a good shot at Anakin, and were forced to follow the two along the river as they duelled on the robots that were working on maintaining the facility. Obi-Wan then flipped on the high ground where Rex and Cody reunited with their general and pointed their blasters at Anakin.

"It's over, Anakin! I have the high ground," said Obi-Wan exhausted.

"You underestimate my power," replied Anakin

"Don't try it," said Obi-Wan

However, Anakin leapt and the two clone officers took the shot, and successfully hit his shoulders and hands, while Obi-Wan sliced off said sith's legs and left arm. Anakin fell onto the ground in pain, starting to steam from the lava.

Obi Wan shouted in anguish, "You were the Chosen One! It was said that you would destroy the Sith, not join them. Bring balance to the Force, not leave it in Darkness!"

Rex picked up Anakin's lightsaber, and left to go to the ships, unable to watch Anakin's suffering. Cody pointed his blaster carbine at Anakin, but it was lowered by Obi-Wan, nodding his head sideways.

"You were my brother, Anakin. I loved you! Rex loved you! Your men loved you, but we could never hate you," said Obi Wan as he and Cody left Anakin to burn.

Obi-Wan went up the Naboo cruiser that Padme had and was greeted by Kix while the rest of the clones headed up to the Venators.

"Sir, I've done all I can but she's not improving. It's like she lost the will to live. We must get her to the medical center, and fast," Kix reported as he went up with Obi Wan to treat Padme.

The Venators and the Naboo cruiser left the Mustafar system, heading towards the station. Just as they left, a lone Imperial cruiser arrived to rescue Anakin.

Naboo System, Kaliida Shoals Medical Center

The fleet of Venator arrived at the medical center, and swiftly, Obi Wan and Kix took Padme to one of the medical rooms to be treated.

After analysing and trying to treat her with various equipments, Kix stepped out of the door to report to the Jedi.

"It's not good, sirs. We can't do anything. The best we can do is to deliver the babies." Reported Kix.

"Babies?" questioned Organa.

"Yes, Senator. She's carrying twins," replied Kix.

"Save them, we must. They are our last hope," ordered Yoda Kix.

Kix then rushed back in to help the procedure with other medical clone officers. The twins were delivered. The boy was called Luke and the girl, Leia, Padme died during childbirth. Kix dropped his head down in sadness as he held baby Leia.

Naboo, Theed

In Bail's ship, the clone commanders once again had a meeting with the Jedi and Senator Organa on the next course of action.

"So what happens to the twins, Generals?" asked Gree.

"Pregnant, she must still appear. Hidden, safe, the children must be kept," said Yoda.

"So do we split them up?" asked Bacara.

Organa stood up, "My wife and I will take the girl. We've always talked of adopting a baby. She will be loved with us."

"The boy will be sent to Tatooine, then," said Cody.

"We have already started constructing our hidden bases. The 212th will be on Tatooine with Obi-Wan, 501st on Yavin IV along with the 104th Battalion, 327th Sky Corp on Kashyyyk, 21st Nova Corp on Hoth, the 91st Reconnaissance Corp will have minor bases scattered around the sectors to listen in on and get intel, while the Coruscant guard will go with you, Master Yoda, to Dagobah. Each base will have a cloning facility of their own, with the Kamino security team guarding the base along the rest of the clones. We'll stay hidden and build up our forces until the time is right," reported Thire.

A medical officer of the Kaliida Shoals Medical Center, by the name of Watcher(A/N: My OC clone), stood up and said, "In my report, the Kaminoan scientists have managed to create an anti-aging serum. It shall be delivered to the individual bases once we have mass produced it there. That concludes my report." Watcher sat back down

Ahsoka stood up, reporting, "I'll get the boys ready to leave for Yavin IV. Is this the last time we might see each other? I know Master Plo will come with me, but is it?"

"Hard to see, the future is. Maybe, maybe not. But the Force, guide us it will." Stated Yoda

"We'll get the boys ready to depart," said Cody as he and his fellow commanders stood up and left.

Dagobah

A lone Acclamator ship landed in the swampy landscape of the planet and out came the Coruscant guards, now renamed Jedi guards (A/N: They are protecting Yoda so it seems appropriate…..I think), along with Master Yoda, to build their new base on the planet, while an outpost will be constructed on one of its moons.

Yavin IV

Ahsoka Tano, of the 501st, led the men to the partially constructed base on Yavin IV. The 104th went along with them. Ahsoka then stood up on one of the crates and made a speech.

"In these dark times, we will prevail! What we are fighting for, is the true Republic! We will build up our forces and together, we shall bring down the Empire! Who is with me?"

The clones shouted, "YES!" as they held up their blasters up in the air.

Hoth

Bacara led his men of the 21st Nova Corp to the hidden base in Hoth and ordered his men to help with the construction, as well as to place sentry duties all around the base. Bacara looked up to the sky with a new sense of hope.

'We can win this war, I can feel it.'

Kashyyyk

Commander Gree led his men of the 327th Sky Corp, along with one of his wookie allies, Chewbacca, to the new hidden base. What he saw was that the hidden base was being constructed with the help of the wookie tribes. Gree looked on with happiness and a sense of hope: a hope that they all needed in this time of darkness.

Unknown Sector

Commander Neyo led his men through one of the hidden outposts for the 91st Reconnaissance Corps. Neyo looked at the base and thought, 'This is it. A new war will emerge. Thank the Force that I have managed to get rid of the biochip on most clones,' Neyo ventured forward to the outpost entrance and entered it with his men.

Alderaan

Commander Stone and three of his men decided not go to Dagobah, but instead took on the mission to protect Leia Skywalker, whose surname now Organa, from Imperial eyes. Stone looked at the sky while the Organas were holding baby Leia.

'Let's hope that the children destroy the darkness the galaxy is in.'

Tatooine

The 212th battalion arrived on Tatooine with their fleet of three Venators, safely hidden underground. The foundation of their base having already been constructed, Cody and his chosen squad of men, which included Waxer, Boil, Davijaan and Wooley, followed Obi-Wan to the Lars homestead to give Luke Skywalker to Anakin's family. Having given the baby, Obi-Wan walked towards the BARC speeder and said to Cody, "Now, we wait until the time is right."

"Yes sir. I know I said so before, but we, the proud 212th Attack Battalion, stands behind you, sir!" said Cody as he saluted, with his men following his example.

Obi Wan smiled and got on the speeder and looked on with hope. A dark era may have begun, but with a sense of new hope.