Corellia:

Obi-Wan finds Amidala talking with some other officers in an officers-lounge.

"Commodore, a word" Obi-Wan says.

"Off course" Amidala says. "Excuse me" she asks the others and joins with Obi-Wan. "How can I help you, general?"

"It concerns my apprentice" Obi-Wan reveals. "And your relationship with him."

"Relationship?!" Amidala is truly offended.

"Do not bother denying it, your highness" Obi-Wan says sternly. "Your feelings for Anakin are strong."

"My feelings for Anakin are private" Amidala growls. "And I take great offense of you violating my privacy, master Jedi. My feelings and my thoughts are my own. And I expect that you stay out of my private affairs hence forth, master Jedi."

"I'm afraid that is not possible, your highness" Obi-Wan counters. "You have, unintentional or not, caused great confusion in young Skywalker. He has lost focus and is unsure where his loyalties lie. For a Jedi, that is dangerous. Especially for a Jedi as powerful as Anakin. Your presence is harmful and damaging. If you will not leave Anakin alone, I will have no other choice but to have you reassigned elsewhere."

Amidala is upset, offended and slightly in disbelief. "Who the hell do you think you are? You can not dictate commands to me; I am the queen of Naboo. You do not give me orders, general."

"I think you will have to reevaluate your position in this galaxy, my lady" Obi-Wan says, now quite serious. "The Jedi Order is the most important ally of the Old Republic. And we require of you to abandon your pursuit of Anakins affection."

"If Anakin has any affection towards me, that is his choice and his choice alone" Amidala says. "And if he choses to pursue those affections, that is his choice to make. Not mine and certainly not yours."

Obi-Wan turns grim. "If you will not listen to reason, my queen, I will have you reassigned to continue this war on the far side of the galaxy. From now on, you will have no further contact with Anakin Skywalker."

Obi-Wan turns and leaves, leaving a highly agitated and frustrated Amidala.

( So what just took place? Well, the Jedi can read thoughts and feelings, so it would be strange that they wouldn't sense that something was going on between Padmé and Anakin. At least, to my mind. So when the Jedi begin to sense that Anakin is emotionally confused, naturally they will take necessary action, right? So how should Amidala react to this? I don't think it would be a compelling character if Amidala simply accepted Jedi ruling on the matter, so I decided to have her actually challenge Obi-Wan and the Jedi decision )

Kenobi enters a lounge where Mace Windu, Kit Fisto and Plo Koon are waiting. Yoda, Ki-Adi-Mundi and Depa Billaba are present also as holograms. Kenobi sits down in a chair to take part in the conference.

"Amidala did not take the news well" Obi-Wan says.

"As expected" Plo Koon says. "She is adversarial in nature and of strong will. It is what makes her a valuable officer and one of the Republics most competent battlefield-commanders."

"Then it is settled" Windu says. "Commodore Amidala is to be reassigned to the defense of Jedah."

"Agreed" Kit Fisto says.

Depa Billaba is still concerned. "Removing Amidala, is it really enough? Are we certain it is enough for Anakin to forget these foolish emotions? By the time he started his training he was already tainted by greed and jealousy. Can we be sure that…"

"Anakin is loyal to the Jedi" Obi-Wan cuts in. "And he upholds our creed. This I assure you. Once this distraction has been removed, he will be able to focus on what is important. His pledge to the Jedi Order is not in question. It is a commitment he takes seriously, I assure you."

"Powerful, young Skywalker has become" Yoda says. "More powerful than he realizes himself. But this war, slowly pushing him down the dark path, it does. Clouded his future is."

"His future is uncertain. That does not make him dangerous" Obi-Wan says in defense of Anakin.

"Can we be sure?" Windu wonders. "We all know what will happen should Anakin be tempted by the Dark Side of the Force. He will be more powerful than any Jedi and there will be no stopping him."

"His destiny lies with the Jedi" Obi-Wan argues. "To be a member of the High Council. I foresee no other future."

Yoda slowly shakes his head. "Careful we must be with young Skywalker. We need him to win this war. But careful we must be, or consumed by this war, Skywalker will be."

Amidala walks through the corridors and reaches a door. She opens it and steps through, finding Obi-Wan in the quarters inside.

"Where is Anakin?" Obi-Wan asks.

"I don't know" Amidala says. "I came here to speak to him before we head for Kashyyyk."

"He is missing" Obi-Wan explains. "No-one knows where he has gone to."

"Missing?" Amidala can hardly believe it. "Why would he leave?"

Obi-Wan takes a look around in Anakins quarters. "I don't know, but I sense a sinister plot is in motion."

"What kind of plot?" Amidala asks.

"I'm not sure."

"Anakin would never leave without good reason" Amidala says. "He knows how significant the battle for Kashyyyk will be. He would only leave if it was truly important. If it could save lives."

"I agree" Obi-Wan says. "But why wouldn't he tell me?"

Mustafar:

A shuttle heads for the planet, enters atmosphere and lands at the Confederate base. Disguised as a mercenary-captain, wearing a gasmask to conceal his face, Anakin leaves the shuttle together with T7 and enters the base. Unknown to Anakin is that Darth Ty'Rahn oversees his shuttles arrival from a balcony higher up.

Ty'Rahn enters his lounge and steps up on a holo-transmitter pad and kneels. Within a few seconds, the hologram of Darth Sidious appears before him ( Sidious is wearing the same metallic mask as in the previous "movie" ).

"Yes, my apprentice" Sidious says.

"Skywalker has arrived as you predicted, my lord" Ty'Rahn says.

"Excellent" Sidious says. "Skywalker will kill the leaders of the Confederacy, after which you will make sure he will complete his journey towards the Dark Side. Grievous will be destroyed at Kashyyyk and then only the Jedi remain. With Skywalker at our side, the Jedi will be annihilated."

"Forgive me, master" Ty'Rahn says, "but shouldn't it be Lady Ventress that should turn Skywalker? She is the one without an apprentice."

"Ventress is a pawn, nothing more" Sidious says. "Her fate has no meaning. Skywalker, on the other hand, can lead the Sith to greatness. With my guidance, Anakin Skywalker will create an empire that will bring the galaxy to its knees."

Ty'Rahn looks up at Sidious. "You intend to teach Skywalker yourself, master?"

Sidious turns to look directly at Ty'Rahn. "Only I am capable of completing his training. Confront him, Lord Ty'Rahn, and turn Skywalker against the Jedi."

"As you wish, my master."

Orbit of Kashyyyk:

The Confederate fleet arrives in force at Kashyyyk. On the bridge of Grievous massive flagship, the crew and officers are truly surprised to find a strong Republic fleet in waiting.

An officer walks over to Grievous. "General, we have spotted an enemy fleet of thirty ships in orbit of the planet. Six of them appear to be a new design of battleship that we have not encountered before. They were waiting for us, sir."

Grievous growls. "We have been betrayed."

Admiral Tarkin studies both fleets on a hologram. "Send in the Star Destroyers. Give them all the fire-support we can muster."

"Yes, admiral" an officer replies.

Both fleets open fire on one another. The six Star Destroyers ( Victory-class ) brakes away from the rest of the Republic cruisers and heads straight for the Confederate fleet, firing all dorsal and flanking turrets.

On Grievous flagship, the maneuver does not go unnoticed.

"The new battleships are leaving formation" an officer points out. "They are heading straight for us."

Another officer turns to a lieutenant. "Inform the fleet to concentrate fire on the enemy battleship taking point."

The first officer turns to Grievous. "Sir, if they lock us down and gets us bogged in battle, they could call in reinforcements to prevent us from withdrawing. We would be destroyed."

"After Geonosis and Ryloth they have no reinforcements" Grievous points out. "If we destroy this fleet, there will be nothing to stop us from attacking the shipyards at Kuat. Inform all captains to continue as planned. We attack! This war ends today."

Amidala is standing on her bridge and watches the Star Destroyers taking a severe beating. One of her officers walks over to her.

"The ship is ready, your highness. On your command, we will engage the enemy."

"Good work, captain" Amidala says. "Now all we have to do is wait for Tarkin to give the order."

The captain looks at the Star Destroyers. "I've never seen shields that strong."

"Each Star Destroyer is a flying fortress" Amidala says. "They carry the shields and firepower of three or four other vessels combined. They were expensive to build and demanded a lot of resources to be built. Let's hope they were worth the cost."

Grievous turns to his crew. "Fire the ion-cannon!"

The Invisible Hand fires its massive ion-cannon and hits one of the Star Destroyers, depriving it of power altogether.

Grievous clenches his fist. "Destroy them!"

The siege-cannon on Grievous flagship opens fire and rips a giant hole straight through the main hull of the Star Destroyer that had lost its power.

A large formation of Confederate Y-wings leave the Confederate fleet and heads for the Star Destroyers.

Captain Fey'lya is standing on a Star Destroyer bridge and an officer walks up to him.

"Sir, eight squadrons of enemy bombers are heading our way."

"Deploy fighters" Fey'lya says.

Out of the belly-hangar of each remaining Star Destroyer, two squadrons of T-19 Torrent fighters are released by each battleship and they fly to intercept the Y-wings.

On Grievous flagship, an officer turns to Grievous.

"Sir! The enemy battleships are entering our formation!"

The five remaining Star Destroyers enter the enemy formation and begin blasting with all cannons available at the surrounding ships.

Fey'lya, standing by the bridge view-ports, turns to his officers. "Launch our bombers."

Each Star Destroyer deploys a squadron of ARC-170's that immediately engage the enemy ships.

Tarkin, studying the battle on a hologram, turns to the officers on his bridge. "Send in the Wookies. Have our fleet standing by. And inform Master Windu that it is time to join the battle."

Leaving the Republic fleet are six corvettes and two squadrons of fighters, all of Wookie design and crewed by Wookies naturally. The Wookies move in to engage the enemy and growl and roar as they do! ( and one of the Wookie pilots does look a lot like Chewbacca; an unnamed cameo )

The Star Destroyers have broken through the enemy lines and on the bridge of his vessel, captain Fey'lya issues a command.

"Turn us around, let's give them another taste."

The Star Destroyers begin to turn back towards the enemy ships once more.

Grievous slams his fist against the tactical-table that depicts the battle. "Those battleships have cut us to pieces! Do not let them cut through our lines again! Concentrate all fire on those ships now!"

Colonel Mara Dendron leads her fighter-squadron through the Confederate fleet towards the Star Destroyers. "This is Scimitar Leader, ready torpedoes and lock onto the bridge. Increase to full throttle and watch out for the cross-fire."

As the Star Destroyers opens fire on the Confederate fleet once more, Scimitar squadron attacks one of the massive battleships.

Three Jedi Corvettes leave hyperspace, together with 12 Jedi Tie Advanced fighters and one older model Jedi Fighter and they head straight for the battle, having arrived behind the Confederate lines.

Mace Windu sits on the bridge of one corvette. "Target Grievous flagship. Lock torpedoes and take out their shields."

On another corvette, Kenobi sits in the captains chair. "Understood, grand master. Take us in."

The three corvettes head straight for Grievous flagship in wedge-formation, surrounded by the Jedi fighters.

Plo Koon pilots the older version Jedi fighter. "Enemy fighters coming at us. Split up and move to attack speed."

The Jedi ships engage the enemy and the corvettes launch torpedoes at Grievous flagship.

Tarkin, as ever watching the battle on a hologram, nods. "The Jedi have joined the battle. It is time for us to move in. All ships, engage the enemy."

Onboard a Twilight-looking vessel, Sebulba curses as always in huttese. Next to him sits Dex.

"About god damn time" Dex says. "Gambit squadron, this is Gambit Leader, full speed and charge your guns. We're moving in!"

Amidala hurries over to her chair on her own ship and sits down. "You know your orders… Engage the enemy."

The three Arquitens-class light cruisers and supporting frigates and corvettes of Amidalas squadron head towards the Confederate fleet, surrounded by dozens of fighter-squadrons racing ahead to engage the enemy.

Mustafar:

In the Confederate command-center, the leaders of the Confederacy follow the battle at Kashyyyk.

"The Jedi have deployed in force!" Viceroy Gunray points out. "Grievous needs reinforcements!"

Wat Tambor, a Confederate leader, studies the battle. "If we commit our reinforcements to this battle, we better win, or we will have lost too many ships and gained nothing."

A human politician is next to speak. "That is exactly what the Republic has done. With so many Jedi taking part in one battle, it is clear that they are desperate. They know that if Grievous defeats them at Kashyyyk, they will be unable to defend Kuat."

Gunray nods. "Then we have no choice. Inform Grievous that he can expect reinforcements in ten hours. Tell him to withdraw to the asteroid-field and hold until Lady Ventress arrives with her fleet."

At that point, Anakin, still in disguise, enters the command-center together with T7. T7 hooks up to a panel in the wall and after a few short seconds, every blast-door leading to the room close shut. Everyone in the room turn around and wonder what is going on.

"What is this?!" Gunray says. "What is going on?!"

At that point, Anakin ignites his lightsaber.

"A Jedi!" someone cries out.

"An assassin!" Gunray says. "Someone, find Dooku! Get him down here!"

Anakin attacks.

( the scene doesn't have to be all too dissimilar from what we see in Episode 3, except that perhaps a few more guards and droids try and stop Anakin perhaps )

Dooku/Ty'Rahn is standing in his lounge and overlooking the landscape when the alarm sounds across the base. He turns, nods, and then turns back to looking at the volcanoes and rivers of lava with no intention of saving the other leaders of the Confederacy.

Battle at Kashyyyk:

Wookie and Jedi fighters join in an attack on a Confederate cruiser, dealing it significant damage.

Gambit squadron gun down several enemy fighters.

The three Jedi corvettes launch another salvo of torpedoes against Grievous ship and destroy the siege-cannon.

Kenobi studies data on a screen. "Grievous flagship has lost its main cannons. Focus fire on their engines."

Mace Windu is shaken around in his chair as his corvette takes some hits. "Understood, Kenobi. We're turning around for another attack-run."

"We're right behind you, grand master" Kenobi says. Then, he senses something, something terrible. "Anakin?"

Mustafar:

In the command-center, Anakin lifts Gunray by the throat and impales him with the lightsaber and then tosses him casually to the side, Gunray slamming into the consoles and screens.

Republic Command-Center, Coruscant:

Everyone are following the events at Kashyyyk. Yoda, sensing a great disturbance in the Force, walks away to be alone. Ki-Adi-Mundi follows Yoda shortly after.

"What is this darkness we sense?" Ki-Adi-Mundi asks. "Why is it hidden in shadow?"

"Something dangerous has happened" Yoda says. "Grown stronger, the Dark Side has."

Ki-Adi-Mundi turns and looks at all the officers and politicians following the battle. "We are being deceived at every turn. Tricked to place our focus away from what is truly going on."

Yoda nods. "This is not Darth Ty'Rahns doing. Manipulating the Force, someone else is."

Battle at Kashyyyk:

Tarkin, as ever studying the battle on a hologram, turns to his officers. "Send in Commodore Constantine and his squadron. Have him target enemy escape-pods, shuttlecraft and medical-frigates."

The officers look at each other, somewhat concerned. "Sir" one of them says, "attacking medical-frigates and defenseless escape-pods is forbidden according to the Articles of War."

Tarkin looks as serious as ever. "We lost hundreds of our finest and most experienced officers at Geonosis and Ryloth. If we are to win this war, we need to deprive the enemy of any advantage they might have. Right now, that means killing their experienced officers to deny them any future advantage. Target the escape-pods, now!"

Republic Command-Center, Coruscant:

Organa is appalled at what he is seeing. "Admiral Tarkin, please respond. Your forces are attacking Confederate medical-frigates. Order your ships to check their targets."

Tarkin appears as a hologram in front of everyone. "Ladies and gentlemen, I was given command of the Kashyyyk forces with explicit orders to defeat General Grievous and give the momentum of this war back to the Republic. I am doing exactly that. Those medical-frigates are currently treating some of the Confederacy's most experienced and accomplished naval officers. If we allow them to escape, they will be in command of new clones and droids within weeks. If we are to win this war, hard decision needs to be made. We have an opportunity here to break the Confederates spine; I intend to take it."

Organa can't believe what he is hearing. "Admiral Tarkin, you will order your troops to only engage legitimate targets!"

Palpatine is next to speak. "Perhaps we should consider what we stand to gain from all of this. We lost many of our finest officers at Geonosis and Ryloth. This battle could very well determine the outcome of the war. If we hope for a swift victory and a quick end to this conflict, then perhaps we should consider depriving the enemy of its leadership. Without experienced commanders, the Confederates can not win."

Ki-Adi-Mundi speaks next. "Chancellor. If we allow this, it will only fuel hatred and promote further atrocities, by both sides. It is a dangerous road that you promote, chancellor."

"If it will bring peace and stability to the galaxy, and secure the future of the Republic, I am willing to let history judge me and my actions" Palpatine says. "Admiral Tarkin, you may proceed. It is time to break the Confederates will, and ability, to wage this war."

Everyone looks around, appalled, afraid, unsure and in disbelief.

To be continued…

So Obi-Wan and Padmé have their argument about Anakin. I think it makes sense for them to have it. The Jedi are also aware of the danger of keeping Anakin around, but they also realize that he is crucial to the war-effort. It is important to remember that Palpatine is still obscuring the will of the Force to the Jedi, making it hard for them to find out how dangerous Anakin is. We also begin to see Tarkins sadistic side, which of course will lead up to him casually ordering the destruction of an entire planet in A New Hope. Anakins raid against Mustafar I think was poorly handled in Episode 3; it seems to me that his fate should have been sealed when he killed the younglings, and not when he killed the Separatist leaders. I think it would have made more sense, and been more effective, had Anakin assassinated the Separatist leaders first, as a step towards the Dark Side, ending with his final fall from grace as he betrayed the Jedi Order and in the end killed children. So that is why I use the assassination of the Confederacy leaders in this story as a stepping stone, a quite significant one, in Anakins eventual fall to the Dark Side.