This is an AU if the Clones weren't replaced. And what if Anakin is the one who will rule the galaxy. Hope you guys enjoy.
Anakin or now known as Darth Vader kneel in Palpatine's presence. The Sith Lord chuckle as he just executed Order 66 to every known Clone battalion commander. Now that the Jedi Order has fallen and the survivors are being hunted down, all according to the Sith Lord plan. He turned to his apprentice with a crooked grin.
"The time has come, to bring this game to an end. The remaining CIS council is on Mustafar." Palpatine told his apprentice "Go and disposed of them. They have served their purpose. Now we have no longer need of them."
"Yes, my Master." Said Vader but something troubles him.
"I sense uneasiness from you." Said Palpatine "What trouble you, my apprentice?"
"Forgive me Master, I been thinking."
"About what?"
"What will happen to the Clone Army?"
"What makes you think that? Why would you care what will happen to them?"
"The Clones have served the Republic since the war started. They're all good soldiers, best of the best. The Empire need their strength and skill, if this new Galactic Empire ever going to survive and see the future."
"It is a shame. However, the Clones loyalty is to the Republic. We'll keep them around for one year."
"One… year?"
"Yes, my friend. Those foible Clones only purpose is to kill the Jedi's. They served their purpose now the war I orchestrated is over, we won't need the Clones anymore. Once we control every planet in every system, they'll used up their usefulness. They're only purpose now is to train human combatants to replace them all."
"Is that right?" Vader face covered by shadow as Palpatine has his back turned to him "Yes, Clones cost a lot, and are inferior to humans since there are unlimited supply of them in our disposal." Palpatine told him as he went on "There's no room for them. Now go and carry out your mission my apparent-"
His word was cut off. Palpatine gasped as a sharp and hot pain hit him. He looks down to see a blue lightsaber impale through his chest. As the lightsaber retracted Palpatine body fell to the ground. He laid there motionlessly, with his face showing a shocking expression. Vader stood over his master body, looking down at him. Showing no remorse nor regret.
"Forgive me 'Master'. The Empire won't keep the peace without the Clones." Vader told his decease master "I've fought by their side during the first year of the war. There are no better soldiers who been through hell except them. They'll serve my new Empire, better than those who aren't battle experience."
Vader turned on the hololink from Palpatine's office. A hologram of Appo appeared "Commander Appo, contact Commander Fox and get both the 501st and the Coruscant Guard on three light cruisers. We're going to Mustafar." Vader commanded.
"What's on Mustafar, sir?" Appo asked his Lord.
"The last remaining Separatists are on Mustafar in hiding. Let's end this war once and for all." Vader answered.
"Yes, sir! I'll contact Fox right away!"
With that the hololink turned off. Vader looked at Palpatine's body once more "The Clones may have pledged their loyalty to the Republic. But they'll still remain loyal and continue to serve under the Empire, my Master. The galaxy will be under my rule." Vader then left the office, leaving Palpatine's body remaining on the floor.
Mustafar
The CIS council monitored as the war is coming to an end. With the Republic forces pushed their troops back, its only a matter of time. One of the B1's turned to the council "Sir, our sensors picking up something coming out from hyperspace." Said the B1.
"Is it Vader?" Nute Gunray asked.
"Not sure. Wait, three ships came out from hyperspace."
"Three?" Aito Laff surprised "What do you mean three ships? Whose ships are those?"
"Three Republic light cruisers sir."
"The Republic?!" Nute Gunray shouted "Sidious said he's sending only Vader to protect us!"
"We been double-crossed!" Said Poggle in Geonosian language.
"Sent the droids outside at once!" Nute Gunray ordered.
Inside the light cruiser in the front of the other two, Vader talked to both Coruscant Guards and the 501st as they prepare for battle "The remaining CIS leaders are in this Klegger Corp Mining Facility." Vader pointed to the hologram map "Commander Fox, you and your men will be the first wave. Me and Commander Appo will join shortly after. This is where you'll land."
"Leave it to us sir. We'll secure the platform by your arrival." Said Commander Fox.
"Prepare to depart for battle. This war ends today."
The Coruscant Guards boarded unto three LAAT/I gunships. As the hanger opened, the three gunships took off. Assenting to Mustafar mining facility. Vader and the 501st loaded onto a single gunship. Following the Coruscant Guards lead.
By the time the gunships landed on the platform, the Coruscant Guards quickly got off. Just then B1's and B2's battle droids exited the facility, spotting the Clones on the platform "Clones! Open fire!" The B1 ordered.
They started to blast away as the Coruscant Guards getting shot at "Return fire! Blast those clankers!" Commander Fox commanded.
The men returned fire. Three B1's and a B2 get shot down. One or two Coruscant Guards get hit at the chest area. Fox moved up as he look back to his men "Bring in the shields!" Ordered Commander Fox.
Several Clones with shields ran up to the front. Blocking the bolts as they begin to move up. Just then a gunship hovered above, Vader ignited his lightsaber. He then jumped out the gunship slice an B2 droid in half. The droids then focus their attention on him as he deflects the bolts. Hitting two droids, he then used the Force to push a row of droids to the sides. Falling into the lava as they screamed. More battle droids came and started to shoot. Commander Appo and the 501st dropped down with cables. Joining their general into the fray.
Several droids get shot down. One of the 501st Clone gets shot in the chest, fell backwards motionlessly. Commander Appo shot a B1 head clean off, then knocked a B2 down with his gun. He then faired multiple shots on it. Vader then cut down few of them. He then proceeded walking with his men following him inside.
The CIS council locked the door. But it was futile since they're already beginning to cut their way through. As the door been breach, both the 501st and Coruscant Guards storm the war room. Shooting down any remaining droids. Commander Fox shot one of the droids right at the head. Both 501st and Coruscant Guards surround the council. Commander Appo and three others 501st Clones escort both Rune Haako and Wat Tambor out from the conference room next door. Shove them to join the other council members. Vader walked inside with his hood still up. Commander Appo join his general.
"My Lord, all the Separatists leaders are accounted for." Reported Commander Appo.
"Good work, Commander. Procced to send a message to the Trade Federation to shut down the battle droids." Ordered Vader.
"Yes sir." Appo walked to the control pads to decommission the droids.
Vader then walked around the council as Nute Gunray clasp his hands "Please, spare us! Lord Sidious promise us peace! We only wanted-"
"Sidious filled you lies. He never intended to help you to bring peace." Said Vader with his voice filled with spite "He used you all to do his dirty work. To destroy the Republic. Bunch of Separatist slims faces."
"Message has been sent, sir." Said Commander Appo.
"Good prepare to leave."
"Sir? What about them?" Commander Fox pointing at the council "Shouldn't we take them back to Coruscant for trial?"
Vader look at them with hate, turned around the only thing he said, "There are no prisoners to take back." Vader grimly responds.
Commander Fox nodded and turned to his men "Blasters ready!" Both Coruscant Guards and 501st raised their blaster rifles "Aim!" Aiming at the council.
"Wait! You-You can't do this!" Nute Gunray plead as Vader along with Appo and some men leaving the room.
"FIRE!" Shouted Commander Fox.
Sounds of blasters rang through the room. It kept going until it finally goes silent. Vader look at Appo "Contact the gunships for pick up." Said Vader.
"Yes, sir." Reply Commander Appo.
"Sir, got word from the light cruiser that a ship is came out from hyperspace." Said one of the 501st.
"What kind of ship?" Ask Vader.
"A J-type Naboo Star Skiff. She's asking permission to land."
Vader look surprised when he heard the name of the ship. There's only one person he knows who could be "Tell them she has permission." Said Vader.
"Copy." The Clone then replies to the light cruisers.
Quickly the gunships arrived. All the Clones board them as Vader talk to Appo "Take the men back to the light cruisers and hold your positions." Vader told Appo.
"What about you Lord Vader?" Ask Commander Appo.
"I'm going to meet our visitor. It won't take too long."
"Is it okay to leave two men to accompany you?"
"Of course."
Commander Appo look at the two Clones by them "You two stay with Lord Vader."
"Yes, sir." They said in union.
As all the troops left, only Anakin and two Clone Troopers remained. The Naboo ship landed, with its hanger opened Padme exited the ship. Seeing her husband Padme and Anakin embrace in a hug.
"Anakin." Padme happily spoke.
"They told me you were coming. What are you doing here?" Anakin asked.
"I was worried about you. Saw the light cruisers orbiting… Obi-Wan came to see me. He told me terrible things."
"Told you what?"
"He said you have turned to the dark side... that you killed younglings"
"He's trying to turn you against me."
"He cares about us."
"Us?"
"He knows... He knows about our child. He wants to help you.
"Help? Is Obi-Wan going to protect you? He can't... he can't help you. He's not strong enough."
"Anakin, all I want is your love."
"Love won't save you, Padme. Only my new powers can do that."
"At what cost? You are a good person. Don't do this."
"I won't lose you the way I lost my mother! I've become more powerful than any Jedi has ever dreamed of, and I've done it for you. To protect you."
Padme looked at Anakin in shocked. The way he was saying. It doesn't sound like her Anakin. But she still refusing what Obi-Wan told her "Come with me. We can raise our child together. We talk about how we could leave all of this behind us. Me leaving the Senate, you with the Jedi Order. We can leave all of this behind!"
"We don't need to run away anymore. Don't you see I have brought peace to the Republic? I've killed the Chancellor."
Padme gasped "You… You did what?" Padme asked.
"I killed the Chancellor. Showed him I'm more powerful than him. Join me Padme, you and me together we'll rule the galaxy. Bring peace and order." Anakin trying to get his wife to join him.
"I-I can't believe what I'm hearing." Padme crying, horrified what Anakin has become "Obi-Wan is right. You've change."
"I don't want you to talk anymore about Obi-Wan. He and the Jedi turned against me. If it wasn't for them, my mother would still be alive. Don't turn against me too, Padme."
"I don't know you anymore. Anakin, you're breaking my heart. I'll never stop loving you, but you are going down a path I can't follow"
"Because of Obi-Wan?" Anakin sneered with hate.
"Because of what you've done... what you plan to do. Stop, stop now. Come back. I love you." Padme plead with tears falling from her cheeks.
Anakin look at his wife, desperately trying to get him to see his wrongdoings. He turned to his men who are watching the whole thing. Even they don't know what to make of it. Nor have the answers to help the solution. He looks back at his wife. Before he could answer, he looked at the ship to see Obi-Wan standing there. Seeing Obi-Wan suddenly awaken something as he glared at Padme "Lair!"
Padme looked behind her to see Obi-Wan. She gasped in surprise as she looks at Anakin "No… It's-It's not what you think…" Obi-Wan walking down the hanger.
"Jedi!" Shout one of the Clones.
"Blast him!" Shout the other.
Both of them shoot their blasters. Only for Obi-Wan used the Force to stop the bolts in mid-air. He then thrust his hand forward, sending them back. Hitting the Clones right at the mid-sections, killing them.
Anakin wasn't fazed one bit "You brought him here to kill me!" Anakin angrily using the Force to choke Padme.
"Let her go Anakin! She didn't tell me where you were, she didn't even know I snuck on board! Let! Her Go!" Obi-Wan demanded.
Letting Padme go. She fell down unconscious. Anakin looked at his old master with hatred "You turned her against me!" Anakin angrily shouted.
"You did that to yourself." Obi-Wan calmly responds.
"You're not taking her away from me!" Taking his clock off.
"You already lost her when you confess what you did. You let you anger and lust for power consume you. You have allowed this Dark Lord to twist your mind until now . . . until now you have become the very thing you swore to destroy."
"Don't lecture me. You knew." Anakin pacing "She said you knew about us."
"That's right. Ever since Geonosis."
"Why didn't you say anything if you knew?"
"I want you to decide what you believe is right. I know the code forbids Jedi's to form attachments. But I want you to decide you have something that I couldn't. I had my change to stay with the Duchess but choose to remain with the Order. If I can change anything, I would've gone back and chose to stay with the woman… who stolen my heart."
"But you couldn't. You had your chance, now she's gone. Because your Jedi code forbids it. My eyes are open to the truth."
"Which truth, would that be?"
"The lies the Jedi have spread. I do not fear the Dark Side like you and the other Jedi's. I've brought peace, justice, and freedom to my new Empire!"
"Your new Empire? So, you really did kill Palpatine. Anakin don't you see what he did? He created the war to get everyone to lose faith to the Republic."
"Don't make me kill you, my Master."
"Anakin my legion is to the Republic, to democracy!"
"If you won't join me. Then you're my enemy."
"Only a Sith could say that. I didn't want this to destroy the bond we made. But I'll do what I have to, for the good of the galaxy." Taking out his lightsaber.
"You will try."
Standing in the bridge of the light cruiser. Commander Appo waited for Vader orders. However, it been over an hour since the Naboo ship has landed and still no word. Appo look at the officers piloting the ship "Any word from Lord Vader?" Commander Appo asked.
"Nothing yet sir." Said one of the officers.
"What about the men with him?"
"Still in the dark, no response." Said the other.
Commander Fox entered the bridge joining Appo "Anything, yet?" Fox asked.
"No. And we can't seem to contact the Naboo ship either." Appo responded which Appo begin to worry behind his helmet "I think something bad has happened."
"How can you be so sure? For all we know, we're on standby until farther orders."
Appo goes silent. He agrees with Fox since they must be ready for any orders. But deep down he knows something isn't right. Until Fox spoken up "I wonder what's going to happen next?" Fox ask himself.
"What you mean?" Ask Appo.
"Now the Jedi traitors been dealt with, and the Republic is now gone. What's going to happen to us?"
"Why you say that Fox?"
"You know what I mean. We've been bred to fight in a war."
"You and the Coruscant Guards are bred to keep the peace on Coruscant. You don't know must what war is really like."
"My men been on some battles off-world you know. Thorn went out fighting, lucky son of a bantha. He was always the coolest out the rest of us."
"I guess so. And to answer your question. Lord Vader think of something."
"You really think so?"
"I don't think." Appo look at his brother "I know."
Soon, they're receiving a transmission "Commander Appo, it's the Naboo ship. It's leaving." They see the Naboo Star Skiff leaving Mustafar.
"Contact the ship." Ordered Appo.
"We can't. It's blocking us out. It's going to jump into hyperspace!"
"Get the turbolasers ready to fire!" Ordered Fox.
"It's too late." Said the officer.
The Naboo ship jumped into hyperspace, past the light cruisers. With everyone silent, Appo broke the silence. He presses his helmet communication "Captain, get the shuttle ready. Gather a small team for departer." Ordered Appo as he walked to the door.
"Where the kriff are you going?" Fox asked.
"Going to the planet surface. Something must've happened to Lord Vader." Answered Commander Appo leaving the bridge.
An Imperial shuttle landed on the outskirts far from the facility. Commander Appo and several Clones from the 501st exited the ship. Appo pulled out a lifeform scanner to hopefully detect his Lord vitals. The scanner beeps loudly, detecting something in front of them.
"This way." Appo lead the way with his men following him.
The scanner beeps gets faster and faster. By the edge he sees a figure laying on the ground. He and few Clones follow him. By the time they reach the figure, they realize it's their Lord. Missing both legs, left arm and badly injured. Appo turned to the men standing at the edge.
"Get a medical capsule, quickly!" Shouted Appo.
"Yes sir! Right away!" Said one of the Clones. They rushed off with Appo and three other Clones remained by Vader's side.
The shuttle landed on Coruscant Rahab Bay platform. Several Coruscant Guards standing on the sides. Appo and members of the 501st exited the shuttle, with Vader's laying on a medical capsule. Floating to the Rehab Center.
Vader lifted up onto a table. Medical droids begin to make new arm and legs for him. Once the operation is finished. Vader wears a black suit and a cape. Commander Appo taking his helmet off look at his Lord.
"Lord Vader? Are you okay?" Ask Appo.
"Commander Appo? Where's Padme? Is she safe?" Vader asked.
"I'm not sure. A Naboo ship jumped into hyperspace. You were the only one we found."
Vader looked at Appo with his eyes full of pain "I felt her." Said Vader weakly.
"Felt what sir?"
"Her life, she's gone." Vader took a few steps "I killed her… I let my anger take over." The room shakes and tremble as if a powerful force is crushing the room "She… What have I done?!"
The room imploded including the droids present. Vader let out an anguish cry as Appo watch his lord with sadness. Once Vader stopped, he looks at Appo "Commander?"
"Yes, sir?"
"Contact to every Clone Commander. I have an announcement to make."
As Vader ordered, every Commander has appeared before Vader. Looking at every Clone Commander he begins his presentation "You all have served the Republic since you were born. For that the new Empire need men like you to keep this galaxy safe. You all will be my Enforcers, to keep the peace, to deliver justice. Commander Cody. You're one of the best Commander's this army has seen. You'll be in charge of the entire Clone Army as the Lord Commander. Do you accept it?"
"I'll be honored sir." Cody replied saluting.
"From this moment on, the Empire military force now under the command Commander Cody, along with every Commander of the new Galactic Empire."
All the Commanders cheered as the dawn of a new era of the Clone Empire has begun.
Well, I hope you all enjoyed this story of mine. Not going to lie, this one is long. Have a great Valentine Day.