A/N: This top section will be where I answer questions from reviewers. TaitanoRules555 asked if I would wait for the Siege of Mandalore to come out and then continue the story. The Siege of Mandalore is the last arc in the new season so I don't think I will be waiting. After I publish this chapter I have another chapter already written and I'm working on the fourth chapter right now. By the time the first episode of season seven airs, I will probably have published my third chapter. I appreciate the review and hope you enjoy the story.

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Star Wars

The Supreme Commander

Chapter 2

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Anakin and Obi-Wan strolled through one of the abandoned corridors of the lower levels of the Jedi Temple. Many Jedi came here to think and clear their mind before the war, but with so many Jedi on the front lines, it was now a relic of a bygone era. It was one of the original floors in the Jedi Temple and used to foster gardens. It was a place where Jedi could find their inner harmony, but around the time the Sith fell, new additions were added to the Temple and it became a place where Jedi would go to be alone.

"So the Chancellor offered you General of the Republic?" Obi-Wan asked one more time to make sure he had it correct. It wasn't that he doubted Anakin was worthy of the job, it was that this role was the most important role in the entire Clone Army. He was shocked that an officer on the High Command didn't get this role. Added to the matter was that the war was almost over and it didn't seem like they would need a Supreme Commander much longer.

Anakin nodded, "he did, and I think I want to take the job."

Obi-Wan stopped and looked around to make sure nobody was around. "Anakin, I'm proud of not only the Jedi you've become but also the man. I don't want this to come off the wrong way, and I know I said I'd support you but-."

"I know what you're trying to say," Anakin said, "Obi-Wan. The talk we had the other night. It saved me from making choices I would have regretted. I felt a darkness growing in me but now," he paused, "now, it's gone. But the Jedi Order and my frustration with the council pushes me to places I don't want to go."

Obi-Wan could only stare at Anakin. He saw the slave he met on Tatooine, he saw the boy that ran at Count Dooku on Geonosis, and now, he saw a man that's won more battles than anybody in the order. He knew Anakin's path wasn't with the Jedi, and he knew that he must let go. His mouth wanted to tell Anakin this was insanity and that the Jedi could change, but deep down he knew that wasn't true.

"Obi-Wan. If you don't want me to leave-."

"No," interrupted Obi-Wan, waving his hands in the air, "if this is the choice you want to make, I will support you. But what will you do after the war?"

Tap. Tap. Tap.

"Intruding, am I?" The green Jedi asked with a chuckle as he sat down on a decrepit bench in front of them.

"Master Yoda," Anakin began not sure how to tell the almost nine hundred year old Jedi why he wanted to leave the order. Yoda wasn't intimidating, but he always had something up his sleeve and he was a bit of a wild card in conversation. Talking to him could be like solving an unsolvable puzzle.

"Want to leave the order, you do." Yoda finished for him and both Jedi were taken by surprise.

"How did you know?" Anakin asked, feeling stupid afterwards. Master Yoda knew everything about everyone.

"A force power few Jedi know," Yoda said, "eavesdropping." A sly grin crept on to his face. Anakin and Obi-Wan chuckled at how even with a conversation like this Master Yoda could put a smile on everyones face. He was serious when he needed to be but the old master had not gotten rusty with his jokes. "A great darkness, I sensed in you. Gone, but always on the outskirts, waiting for weakness."

"I feel as though the Jedi Order and I have some philosophical differences," Anakin confessed.

"That's a big word," Obi-Wan muttered sarcastically and he ducked Anakin's hand coming towards the back of his head.

"Yes. Failed us, the Jedi code has. Address these concerns, after the war, we must. But leave the order, perhaps a smart decision, for you it is. Be with your wife and child, you should."

Again, Anakin was surprised, and he turned around to Obi-Wan who was equally as shocked. If Obi-Wan didn't tell Yoda, who did?

"Safe with me, your secret is," Yoda said, "used your love for another as a strength, you did."

"Master who told you about this?" Anakin asked. The only other person who knew was Palpatine and he didn't imagine he would have shared that secret with Yoda.

"Known for awhile, I have. Used you as a test dummy, I did. Attachment, proved it wasn't all bad."

"I think you resorted to fear because you didn't think you could trust us with this knowledge," Obi-Wan explained, "if we were here to support you then you wouldn't have given into those emotions."

"Made up your mind, you already have. Take the Chancellors offer, you should," Master Yoda said.

"You really want me to leave the order?" Anakin said in shock. Never in a million years did he think Master Yoda would just let him leave. This was a Jedi who had spent more than three quarters of a millennia in the Jedi Order.

"Anakin, there is always a place for you here in the order. I hope that after the war is over, you might return to us. But the position in front of you helps everyone out. You get what you want, the Chancellor has a talented former Jedi leading the military," Obi-Wan said.

"And get an ear in the Republic High Command, we do," Yoda pointed out.

Anakin frowned, "I'm not going to be your puppet in my new position."

"No. But have a good relationship, we must. The Sith, infiltrated the Senate, they have. Certain of it now, I am."

Anakin frowned, Obi-Wan had spoken before of the phantom Sith in the Senate, but he was never sure whether he could believe what Count Dooku had told Obi-Wan years ago on Geonosis. He saw where they were going with this and it was actually a brilliant idea. "So you want me to get close to the Senate to find out who the Sith Lord is?"

"Act angry at each other, we must. Your contempt for the Jedi Order, draw out the Sith Lord, it may," explained Master Yoda.

Anakin had to admit it was a pretty solid plan. The Sith couldn't resist possibly recruiting the Jedi's poster boy after the death of Count Dooku. He just had to play his role and make sure it was a convincing act.

"I'm sure the Chancellor could help us thin out the crowd," Anakin suggested.

Obi-Wan and Yoda looked skeptically at each other. "Anakin," Obi-Wan began, "we need to keep this between us three. The Chancellor could say something to someone and next thing you know, the Sith Lord is alerted."

Anakin frowned, "well if he's going to be my new boss I should keep him informed. He's been my oldest friend I can't keep him in the dark about this. What if the Sith Lord targets him?"

"Then why hasn't he yet?"

Anakin didn't have a response to that. It was rare that Anakin didn't have a quick quip or a sarcastic comment. Obi-Wan had a point, the Chancellor hadn't been targeted yet. The Sith Lord could be biding his time. But at the same time, there were many times throughout the war he had a chance. The Battle of Coruscant would have been a perfect time to strike.

"And if you tell the Chancellor, the Sith Lord might target him," reasoned Obi-Wan. Anakin had to admit that was true.

"Confusing, these times are," stated Yoda grimly, "above suspicion, nobody is."

"I will trust you on this Masters," conceded Anakin. He wasn't sure if this was a good idea, but he had nothing to lose. Plus, what the Chancellor doesn't know can't hurt him. The Chancellor was his friend, but if telling him of this revelation put him in the crosshairs of the Sith Lord then he had to keep him in the dark.

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Sheev Palpatine looked up from his desk when the automatic doors opened and he put on a warm smile when he saw Anakin Skywalker walking through the doors. He was careful not to probe too hard into the Jedi's mind to feel his emotions out of fear for him feeling his force sensitivity. He could feel the Jedi was a little stressed, but also somewhat relieved.

"Have you made a decision my boy," he asked, as he watched the Jedi approach his desk.

"I have. I announced my resignation from the order," he announced with a smile. Waves of joy seemed to radiate off the boy and Palpatine smiled.

"And how did the Jedi Council take it?" Palpatine asked curiously. Already plotting what he could do now that he had gotten the boy out of the Jedi Order.

"Not very well. They didn't support my decision and Master Windu in particular was pretty angry. They don't like how I chose the Clone Army over the Jedi Order."

Palpatine smiled. This had all worked out so well, and now he could begin to glorify Skywalker in the publics eyes and show him what life not bounded to a Jedi Code was like.

"I imagine Master Yoda was not pleased either?" He asked, trying hard to hide the smile that was creeping onto his face. This plan was going perfectly. It was actually easier than what he had planned out before.

"No. He said I was making a dangerous decision and that I was in danger of falling to the dark side. The Jedi never trusted me, and their reaction to my decision shows it. Not even Obi-Wan supported my decision."

"I'm sorry that none of them see that this is best for you," Palpatine said, standing up from his desk and approaching his soon to be apprentice. He put his hand on his shoulder and looked out the window of his office. "Ending the war will help the trillions of citizens that benefit from this Republic."

"I know, and that's what I'm here for. Once we take out General Grievous and the Separatist Council, we can negotiate peace with the Separatist Parliament."

"Yes, and that is exactly what I need you to do. General Grievous is hiding out on Utapau. You, your troops, and an entire armada will blockade the planet and prevent him from escaping. You will crush his droids and do what the Jedi could not. You will bring peace to this Republic."

"Yes Chancellor. Will I have any Jedi helping me with this task?"

"No. Best to have them stay away so they don't screw up the operation," Palpatine said as he returned to his holopad, "Admiral Yularen will lead the blockade and you will lead the ground forces."

"Understood," Anakin said with a bow.

"Now go. Lead the Clone Army to victory and bring peace and prosperity back to this Republic."

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"I left."

"What?"

Padme hadn't seen Anakin in thirty-six hours and the first thing he says to her is he left? Even a radar technician would be able to figure out what Anakin was talking about.

"Don't be mad I can explain," Anakin said waving his hands in front of him, expecting some sort of outburst from Padme.

Padme laughed, "I'm not mad. We can finally be public about our relationship. That's all I've really ever wanted. Plus all the whisperings of me whoring around from the opposition will be put to rest."

"Well that's the problem," Anakin began, rubbing the back of his head, "we can't just yet."

"Why not," protested Padme, "are you worried about how this will make you look in front of the other Jedi?"

"No, no," Anakin exclaimed, "I just- I can't tell you everything because it would put you in danger. All I'm going to say is that I'm playing a dangerous game right now. The worst thing you can do is reveal our connection."

"Anakin," Padme said, basically shouting, "we've been married for three years, you know you can trust me!"

"Padme, I'm serious. I never keep anything from you. You know I'm always up front with you about everything. When I keep something from you, its because I love you and want to keep you safe. The fate of the galaxy lays on me keeping my mouth shut. All I can tell you is don't trust anyone in that Senate building.

"Anakin I work with these people, I can't not trust them!"

"Padme. From the janitors who mop the floors all the way up to the Supreme Chancellor, something is going on and I need to get to the bottom of it. Until then, work like you usually would, but don't give up any information about me."

Padme was overwhelmed by the confusion she now felt. She didn't know if it was the pregnancy or this revelation but she started to teeter on her heels and Anakin had to grab her to keep her upright. This was a lot for Anakin to drop on her.

"Ana-," Padme began but she was cut off by Anakin's poor attempt at a soothing voice.

"Padme, you need rest. What you don't know can't hurt you. I wanted to come say goodbye to you. The Chancellor made me the Supreme Commander of the Clone Army. I'm headed to Utapau to destroy General Grievous and his forces."

"Anakin you are not helping me by saying that!" Padme yelled. Anakin always came home, but now that she was pregnant, she always worried that their child could potentially grow up without a father.

"That's why I'm the soldier and you're the glorified public speaker," Anakin teased.

"Who drugged me up enough to marry you," Padme teased back.

Anakin smiled and didn't say anything. He kissed her on the forehead and looked towards Threepio motioning for him to get Padme's handmaidens to get her into bed. With one last glance, he walked back towards his fighter and departed for his flagship.

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A blue blade swung through the air cutting down the last Mandalorian guarding the throne room. Ahsoka entered the room and saw a familiar Zabrak sitting on the throne, surrounded by Mandalorian warriors who had their weapons pointed at her. Her small strike team had been successful in infiltrating the palace.

"I was expecting Kenobi," Maul said with some disappointment in his voice, "why are you here?"

"It's over Maul, your rule is at an end. Surrender, and the Republic will show mercy," Ahsoka commanded as she pointed her saber main saber towards the throne. She could feel his eyes studying her. A cold sensation washed over her body as he stood up and walked towards her. She put up her hand to keep the troopers behind her steady.

"You poor girl. You know nothing of the Republic you serve under," chuckled Maul. He unleashed a wave of force energy and it took everything Ahsoka had to not get pushed back. Her troops slammed against the wall and fell unconscious.

"What if I told you that there is a Sith Lord in your midst? Controlling everything since the start of this war."

"I don't believe a word you say!" Growled Ahsoka as she lunged towards Maul. He ignited his sabers in time to block the strike. He countered and a series of parries ensued with neither side giving an inch.

"But it's true. I was his apprentice before I fell to Kenobi's blade. Do you know why I disappeared from Mandalore? He was worried I would spoil his plans. He came here and tried to finish me off. The Separatists were always one step ahead of you despite their poor intelligence and weak army."

Ahsoka flipped away from him and disengaged her lightsaber, curious to hear what Maul had to say. He disengaged his saber and continued.

"My operation here should be the least of your concerns. The Sith Lord sent the Jedi here to do his dirty work. You are being played," Maul said with a sadistic laugh.

"Subdue her!" He commanded and the Mandalorian troopers next to him shocked her unconscious.

"What about the Clones sir?" A Mandalorian warrior asked.

"Imprison them as well. The more hostages the better," Maul said as he walked back to the throne. If he could turn the Jedi's sights on his master, they would completely ignore his operation and it would buy him time to consolidate his rule and start his black market operation up. Ahsoka Tano could be his tool to distract the Jedi.

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Anakin Skywalker stood on the bridge of his new Victory-Class Star Destroyer and looked out the viewport. His armada contained three Victory-Class Star Destroyers, and fifteen Venator-Class Star Destroyers. Along with those he had three medical frigates and six support cruisers. They had enough ships to blockade the planet and prevent any escape for the Separatist forces.

"Supreme Commander, we are coming out of hyperspace," the Clone naval officer said as the ship slowed and they dropped out of hyperspace outside of the Separatist fleet.

"All batteries fire," commanded Skywalker as the massive fleet began raining fire down on the Separatist warships. The Separatist fleet was no match for the intense firepower of the Armada and the ships quickly fell one by one. "Admiral, begin descending into the atmosphere. I want gunships with fighter escorts ready. Scramble all communications in and out of the system."

"Yes sir," Admiral Yularen said, getting to work on carrying out Skywalker's orders. Anakin preceded down to the hangar bay. He passed Clones running to their stations and he quickly made his way to the hangar.

"Skywalker, you are clear to begin landing sequence. Stay safe," said Yularen's voice through his comlink.

"Same to you Admiral," Anakin said as he hopped into his straighter. "Landing force this is Skywalker. Group leaders, check in."

"Delta group check."

"Alpha group standing by."

"Beta group check."

"Gold group ready."

"Fighters away," Anakin said as he punched the accelerator forward and lifted out of his crusier. Fighters and gunships poured out of the Destroyers and headed towards the planet.

"Delta and Alpha group, escort the gunships to the rendezvous point at capital city and lend air support to landing units. Beta and Gold groups, form up behind me and engage the remaining enemy fighters."

"Sir, we have enemy fighters at point three and point six."

"Gold group, peel off and take the fighters at point three, I'll take the fighters at point six. Beta group, cover my tail."

Anakin sped towards the enemy fighters, taking out three on his first pass. Weaving and rolling to avoid lasers and ships.

"This is Gold two, we lost Gold Leader and Gold Thirteen."

"Gold two you are now Gold Leader, go for a second pass," commanded Anakin as he jerked the yoke to quickly turn around and go for a second pass.

"This is Beta Leader, we lost Beta Nine."

"Things are gonna get messy up here. If your leader is down the next number is in command. We must eliminate all fighters to prevent enemy air attacks." Anakin commanded, while taking out four fighters and letting his wing men take out the rest.

"Beta squadron, regroup with the blockade and provide support for our Star Destroyers. Gold Group, I am en route to support."

"Copy that."

Anakin sped towards the dogfight. He narrowly missed being blown to pieces by a laser. The enemy ships were moving closer to the atmosphere and had started to disappear into the clouds.

"Gold group, stay sharp," warned Anakin. He felt a warning from the force. "Take evasive action!"

A swarm of fighters appeared out of the clouds and Anakin managed to punch a hole through the swarm and dipped down into the sky where he could see. He had two fighters on his tail and he couldn't shake them. He looked at his control panel to see that they had fired their missiles at him.

He shot down towards the ground and at the last second, pulled up and released the spare parts. The missiles blew up the parts and he turned around and fired on the fighters destroying both of them.

"Gold Leader, status report," demanded Anakin, furious that these fighters had come out of nowhere.

"This is Gold Seven. We lost twenty fighters. The droid ships are gone but we suffered heavy losses."

"Take what remains of your team back to the Star Destroyers to reinforce the blockade. You did well."

"Will do Supreme Commander, good luck down there."

Anakin sped towards the rendezvous point. "R2, scan for enemy anti-aircraft guns and patch me through to Alpha group and Delta group."

R2 beeped an affirmative. Nothing came up on the scanner fortunately.

"-rk two and three," came Delta Leader's voice.

"Delta and Alpha Leader this is Skywalker, we dispatched with the fighters. Is it clear to land?" Anakin asked as he approached the landing site. Already he could see the ground battle had begun.

"Yes Supreme Commander, we have begun our bombing runs and the droids have retreated into the hangars."

Anakin began flying into the sink hole that the Separatists were based in. He landed behind his line and hopped out of his fighter. "R2, take the fighter back to the ship but be on standby to come back."

R2-D2 whistled and the ship lifted off back towards the fleet. Anakin sprinted to catch up to the action.

"Commander Appo," Anakin said into his wrist comm as he hopped onto a lift, "status report."

"We are pushing the droids back. Reports are coming in that General Grievous is near your location. Take lift E7 to the third floor and you should come across him."

Anakin got off the lift at the bottom and sprinted down the hallway. He came across the lift Appo had mentioned and the doors swung open. He was met with the towering metallic body of the dreaded cyborg General Grievous. He was flanked by two magna guards. For just the second time in the entire war, Anakin was face to face with the leader of the Droid Army.

"Skywalker," coughed Grievous, "we meet again."

The magna guards move to engage him and Anakin quickly dispatched the first one. He noticed the cyborg was making a break for another lift and Anakin pushed the other guard into a wall and raced to catch up with him. Grievous entered a lift and the door shut before Skywalker reach it. He spotted a lift down the hall and took it down to the ground floor where Grievous would most likely have gone.

The lift doors open and he came upon an open, two story hangar. He stepped out and spotted the Droid General running towards a shuttle. Anakin quickly used the force to cause the bridge overhead to collapse. Crushing the shuttle and preventing him from escaping.

"General Grievous. For your reputation, I thought you would be less of a coward," Anakin sneered, igniting his lightsaber.

"I will make you wish I had escaped," Grievous threatened, separating his two arms into four and drawing his lightsabers. Anakin had heard Obi-Wan talk about Grievous and he knew what to expect. But to see it in person still threw Anakin off. Nevertheless, he needed to eliminate Grievous so he could bring about the end of the war.

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A/N: Quite the cliffhanger right? I feel like this chapter was a little rushed but I just had to keep things moving and set up some other aspects of the story that will be important down the road. I guess what I'm trying to say is I apologize if the pacing was a little off. I also should note that yes, in canon Ahsoka and Maul's duel takes place during the Battle of Coruscant but I decided to move it back so it was concurrent with Anakin being sent to Utapau. It makes better sense for my story. I added the Anakin and Padme scene while I was writing this note as an afterthought. Chapter 3 will start to tie things together and should make some more sense. I'm gonna work on my pacing for that chapter and try to slow things down. As always, any constructive criticism is much appreciated! Thanks for reading!