Spectre: Another chapter coming up! Gonna take a long break. Since I got college works. Check the AN at the end for more details!


Chapter 39: Conspiracies and Confrontations.

Boots thudded along the hallways as more clones rushed to reinforce the squads Maul had bloodied. Rex himself was heading down to deal with the Sith since Ahsoka hadn't reappeared and Maul was the clear and present danger.

As he was bringing up the rear of the formation, one of Ahsoka's droids shot out from the shadows to collide into him. "Hey. Hey! Out of the way!"

Another one of the droids dashed past them to interface with the ship and seal off the blast doors there, cutting Rex off from the rest of his unit. One by one they sealed until he was locked into an impromptu holding cell.

"Are you crosswired!?" Rex yelled at the droids for their sudden interference.

"Even the order removed the compassion that clones have...", Plo Koon muttered, wondering if this too applied to the 104th.

The droids simply beeped several times before one of them displayed a recording of Ahsoka. "Rex. I think I know what's happening. I saw your report on Fives. It isn't your fault. You were programmed, your mind was altered to do this when you were very young. I can help you."

"Programmed? Like droids?", Caleb asked, resulting of him earning a reluctant nod from Depa.

"We are being forced- No, programmed to follow certain orders. Like droids..." Rex grimaced, burying his head into his hands.

Rex drew his pistol and pointed it straight at the droid once the recording finished. "Where is she?"

"I'm right here."

Rex's skin crawled as Ahsoka announced her presence from right behind him. As he spun to face her, he inadvertently exposed his back to the droid. A mistake he paid for in full when the droid unsheathed a stun prod and electrocuted him.

"Arrrggghh!" Rex screamed in pain as the sudden surge of electricity was strong enough to bypass his armour's shielding and zap him directly. Shocked into unconsciousness, Rex sank to his knees and toppled forwards where Ahsoka caught him.

"Careful! We're trying not to hurt him?" Ahsoka chided her droid, reminding them they were trying to fix her friend not fry him from the inside.

She gently lay the comatose clone commander on top of two of the droids and began walking towards the medical bay. Her droids had locked down all the doors leading there but already the clones were starting to cut their way through the barricades.

"Okay, they got Rex. So now they just need to get that chip out of him and he can tell everyone to stop?" Padme asked in a hopeful tone.

"Unlikely. Except he gave the order that anyone who disobeyed that Order 66 will be executed too. The rest of the ship will still be trying to kill them both." Mace's reply shot her hopes down immediately.

"So what can they do?" Caleb asked.

"R7, run a scan, see if you can find the inhibitor chip the report talked about." Ahsoka instructed as she continued keying commands into a console panel. The still comatose Rex lay on an examination table in the med bay as the scanner warmed up.

As the scans progress and her astromech processed the data, sad beeping came from it as it couldn't detect the chip even with the med bay's most advanced scanners. Ahsoka frowned but refused to give up. "But the chip has to be there. Check again."

She bit her lip as the scans continued to come up negative. Time was running out for them, already the clones had found the med bay and were trying to breach the doors. Her droids had done their best to lock it down, but it would not hold forever.

Drawing upon her Jedi training once more, she pushed down the rising panic and moved to Rex's side. If technology could not help her here...

"Trust in the Force, Ahsoka...", Anakin encouraged her.

Placing her palms on either side of Rex's head, Ahsoka closed her eyes and tapped into the force, willing it to work with her to reveal the truth. "I am one with the force and the force is with me. I am one with the force and the force is with me…"

As the force did its thing, the unconscious Rex began to mumble the mantra as well. The strain showed on his face as Ahsoka's intervention began messing with the inhibitor chip's functions. A small beeping sound came from the monitor as the scanner suddenly picked up a spike of unusual activity inside his brain, signalling the location of the inhibitor chip.

"She's found it!", Kit Fisto exclaimed in relief.

"The answers to our questions...", Mundi added.

"You found it!?" Ahsoka's eyes snapped open and turned towards a viewscreen displaying the results of the scan.

"R7! Get him under and remove that thing!" Ahsoka instructed and began working on the console again.

When her droid beeped its uncertainty, Ahsoka shook her head. "I don't know if it'll work, but if it doesn't, we're dead anyways."

Once more she pushed her uncertainty down as the med bay prepared for an emergency operation. Sparks flared as the clones outside were almost through the doors. Ahsoka grit her teeth and drew her sabers again while her droids worked on Rex.

"They have to get the chip off his head and fast", Saesee Tiin exclaimed. "She would not last long against groups of the 501st"

Rex and Anakin's heads sank at the thought of them trying to shoot down the former Jedi.

Finally, the worst came to pass as the doors started unsealing slowly. A clone ducked under the door to push it up the rest of the way, while his compatriots began filling the air with blaster bolts.

Ahsoka's sabers flashed as she deflected the bolts away, not allowing a single one to touch her or hit Rex by accident. Thrusting her hands forwards, she delivered a powerful force push that sent some of the clones tumbling backwards.

Alternating between force abilities and using her blades to deflect incoming fire, she held her ground as best she could but more troopers continued pouring.

Behind her, Rex was starting to stir. As he came to, his hands began reaching for his blasters immediately.

"No...", Rex worried for the Commander, not wanting to see himself shoot her in the back unsuspectedly.

"They got the chip? Tell me they got the chip in time." Caleb muttered.

A blaster bolt made it past Ahsoka's defence, striking her and causing her to drop one of her lightsabers. As the volume of fire headed her way intensified, she was forced backwards, doing her best to hold off the clones with just her one good arm.

"Ahsoka...hold firm!", urged Plo Koon, praying for the Force to protect her when he could not.

Just when she thought it was over, several blaster bolts shot by her head from behind her, nailing the attacking clones and downing them instantly, including the one holding the door open. Without his interference, the door sealed shut under the guidance of her droids, one of which began welding it down tight.

Ahsoka swung around to find Rex fully awake, twin pistols in hand and shaking. The clone commander was breathing hard and continuing to point his guns in her direction.

"Rex? Are you okay?" Ahsoka asked.

"Y-yeah. I'm okay." Rex took another deep breath before lowering his pistols.

"They finally did it...", Anakin spoke out in relief.

"Sorry for what happened earlier." Rex apologised and gripped the side of his head where the chip had been removed. His mind was his own again but he was still reeling from the aftereffects of the biochip's activation.

"I almost killed you…" Rex muttered softly, barely able to believe the events that transpired despite living them.

"How widespread is this?" Ahsoka asked, partly to get his mind off it and partly to get answers on how deep the conspiracy went.

Rex's face fell and he took another shuddering breath before answering. "Commander… it's all of us. The entire grand army of the Republic has been ordered to hunt down and destroy the Jedi knights."

The two of them lapsed into silence as the implications weighed upon them. Only the sound of clones beginning to cut through the doors reminded them that they were both deep behind enemy lines and the situation was only going to get worse.

"We...we were only tools to dispose of the Jedi we had fought alongside with for years?", Rex grimaced in realization. "By the Kaminoans?"

"But how could we have missed this?", Mundi asked in disbelief. "All we could surmise is that-"

"Don't you get it? The Kaminoans have worked with Dooku after Sifo Dyas was dead!", Obi-Wan told his fellow Jedi, while trying to deny how much they have been blinded by both the war and the Sith to no avail. "By using a known Jedi killer and Senator Amidala's would-be assassin as the perfect specimen for the army, Dooku and Sidious have supplied the Republic an army to wipe the Jedi without our knowledge!"

"And that we did not try to look further in the matter only gave time for Sidious to manipulate everything in his favor", Shaak Ti realized this as well. "Fives...I shouldn't have stopped him..."

"The Kaminoans could have done something to Fives that have him act erratically for him to be labelled as a threat", Obi-Wan theorized, recalling what Anakin and Rex told him during that day. "Essentially a cover-up by both the Sith and the Kaminoans, when he could have told all of us what he knew..., but we were too blind to see it"

Shaak Ti shook her head, her sorrow replaced my both anger and dismay as she realized what the Kaminoans have done to the Clones. "I will speak to Consular Nema regarding the matter of the inhibitor chips. And we will question Lama Su and Nala Se of all of this once we have known the truth"

"Master Ti, if I may, I wish to join you in your venture at Kamino", Plo Koon spoke up to the surprise of everyone. But his one dictated both flared anger and dismay. All this time, the Clones were essentially expendables to the Sith and were no different than droids. And this was too much for the Kel'Dor master to bear, and whatever indifference he had to the Kaminoans became slight hostility, especially when they merely saw them as property sent out to die in the front lines. "I also would like to have a word with them. Personally"

Ahsoka couldn't help but gulp at Master Koon's total change of demeanor, especially when there were very rare instances of him being this angry. But she could not blame him. Cody, Rex, Jesse, Bly and many others were good men acting against their own will.

And they want nothing more than to see. them free from the Sith's slavery.

"Tread carefully, Master Koon", Luminara advised her fellow Jedi. "They could easily be unknowing pawns of the Sith without knowing what their true motivations are"

"But hardly innocent in any degree, Master Unduli", Master Fisto supported the Kel'Dor Master's decision"

Depa pondered for a moment before she spoke out her thoughts. "The entire war was carefully orchestrated to sow the seeds of the future empire. To bring the galaxy into enough chaos and the people will willingly bow down if it means peace and 'freedom' from future conflict."

"How are we gonna get out of here?" Rex asked as the clones outside were almost done cutting through the door. Getting off the operating table, he put on his helmet again and drew his weapons.

"I have an idea." Ahsoka said.

"Which is?"

"Just set those things to stun. We're not trying to kill anyone." Ahsoka replied.

The audience only looked at Obi-Wan and Yoda awkwardly, having seen the two slaughter dozens of Anakin's clone troopers. "In our defense we do not know of the inhibitor chips"

"Yeah well, tell that to them." Rex muttered before doing as she said and thumbing his weapons' non-lethal setting on.

"They're almost through…" Raising both pistols, his fingers tightened on the triggers as the cutting torches on the other side reached the top of the door and began cutting horizontally.

"Wait. Wait… now!" Ahsoka launched a super powered force push as soon as the doors were breached, sending the slab of metal flying outwards and bowling over the clones in the way.

As the others tried to close the breach and open fire on the med bay occupants, they were met with precision fire from Rex, all of them falling before they could get off a single shot


At one of the many bridges of Mustafar, a robed man watched over the distant sun shrouded by dark clouds. Lord Vader watched the lava below him, his mind descending into memory lane. Regret and self-loathing began to consume him as his eyes began to shed tears of everything that he had done.

Obi-Wan and Padme painfully realized that Anakin was still out there, and they both looked at him, only for the Jedi Knight to look away in shame and regret for all he have done.

"The time for regrets have passed", Mace spoke in a neutral tone. "Once a single step was taken onto that road, there was no going back"

Ahsoka and Rex shook their heads of the thought of their best friend whom they thought was beyond redemption.


At the Senate Chamber, Yoda entered the room with the intention of confronting Darth Sidious. Two of the Emperor's royal guards attempted to restrain the Grand Master, only for them to be pushed back against the wall, knocking them out.

"Without a bat of an eye", Caleb said, fascinated of Master Yoda's abilities.

"I hear you have a new apprentice you have, Emperor", Yoda told the seated form of Palpatine, with Mas Ammeda standing beside him. "Or should I call you, Darth Sidious?"

"Master Yoda...", Palpatine greeted the Jedi Master, though he was displeased to say the least. "You survived"

"But I could not say that many others shared his luck", Mundi whispered to Master Tiin, who nodded.

"If Master Windu could best Darth Sidious, then surely Master Yoda would too?", Padme asked, hopeful.

Shaak Ti shook her head reluctantly. "Both Master Yoda and Master Windu have a different fighting style. While Vaapad managed to best Sidious for his use of the Dark Side, I do not know if Master Yoda would be capable at doing so as well..."

"Have faith in him, Master Ti", Plo Koon encouraged her. "We cannot know until we could see it for ourselves"

"Surprised?", Yoda asked almost mockingly."Your arrogance blinds you, Master Yoda", Sidious mocked him, carefully extending his hands. "Now you will experience the full power of the Dark Side!"

A surge of lighting fired from Palpatine's hands struck the Grand Master's body, who collided against the wall and seemingly knocking him unconscious.

"MASTER YODA!", most Jedi shouted in complete dismay at the Sith Lord's brutal attack.

Ammeda took his leave as Sidious walked over the Jedi's downed form, cackling. "I have been waiting for a long time for this...my little green friend", Sidious mocked him, as Yoda's eyes opened and he began to get up. "At last the Jedi are no more!"

All Jedi frowned at the Sith Lord's proclamation, reminding themselves that all is not lost. Anakin hatefully glared at the Emperor, vowing he will deal with him later.

"Not if anything to say about it...", Yoda breathed out, before quickly extending his hand towards the Emperor. "I HAVE!"

Sidious could only yelp as he was pushed back, colliding with his chair. "At an end your rule is...", Yoda continued. "And not short enough it was"

The Jedi were all hoping that Yoda would be able to deal with the Emperor, even despite the future's message for them.

Sidious got up from the tremor and leapt towards the exit, only for Yoda to do the same as he stood in the Emperor's way. "If so powerful you are, why leave?", Yoda challenged him, igniting his emerald lightsaber.

Yoda could only watch himself intently, wishing to know how he would fare against Sidious. Especially as to how to confront him in the impending fight against him.

"You will not stop me", Sidious sneered at the little green midget, igniting his crimson saber as he proclaimed. "Darth Vader will become more powerful than either of us!"

"By corrupting the Chosen One, Sidious has gained the most powerful apprentice that any Sith Lord would desire...", Windu said out loud, observing the two on screen.

"Faith in your new apprentice, misplaced may be", Yoda said, pointing his emerald blade at the new Emperor. "As is your faith in the Dark Side of the Force!"

Sidious raised his saber, prompting Yoda to leap and take him from behind. Blocking his move, Sidious forced Yoda back, the latter using the podium as an obstacle to land as he blocked Sidious' saber.

And the Sith Lord's maniacal laughter hounded the entire room.


Padme got off of the ship as she landed on the mining facility's landing bay at Mustafar. She received a transmission saying that Anakin would be here. Sure enough, she saw him coming out of the tower to come and see her. Padme stumbled down the landing ramp into Anakin's arms."Anakin, than god you're alright." She said as she embraced him before she turned to face him, worried.

"She has no idea what the General has done, has she?", Rex reluctantly asked Ahsoka, but was only met with silence.

"And to think his attachment led him here", Mace spoke out in disapproval.

"What are you doing out here?" Anakin asked, surprised by her appearance all of a sudden."I was so worried about you, Obi-Wan told me terrible things." She informed him as he appeared to be confused on what she had said to him.

Anakin held his wife's hand, hoping nothing bad will come out of this exchange in his already volatile future's state of mind.

"What things?" He narrowed his eyes at her, not liking where this is going."He told me...that you turned to the Dark Side." She recounted as Anakin looked down. "That you killed Younglings!"

The Jedi tried to erase that memory from their heads when they first saw that, and the horrible memory came crashing back on them

"Obi-Wan is trying to turn you against me." He pointed out to sway her to him.

Obi-Wan was pained at hearing this. "Anakin...I would never.."

"He cares about us." She replied, hoping for him to understand.

"Us?" He asked, almost incredulously.

"He could have told us as well...", Ahsoka added, trying to be optimistic at whatever outcome that will come for later.

"He knows...about our child..." She said as her husband looked away. "He wants to help us! Anakin I want is your love..."

"Love won't save you Padme! Only my new found power can!" He boasted, in order to assure her that everything will be alright.

"No power is worth sacrificing the life you knew...", Luminara lowly uttered.

The Jedi Knight looked at his hand, of all the blood he had spilled throughout the duration of the Clone Wars. He only wished to be powerful to protect everyone he cared the most, but he would never reach the lengths of the crimes he had watched.

Especially when a bastard of a Sith Lord still walks the galaxy

"At what cost?! You're a good person! Don't do this!" She begged, but her pleas only began to light the fiery hatred within the man she loved.

"I won't lose you the way I lost my mother, the way I lost my family." He told her, trying to sound reasonable "I am becoming more powerful than any Jedi has ever been, and I am doing it all for you, to protect you."

Anakin turned to Padme. "I wouldn't do any of this...you have to believe me..."

"Just come with me! Help me raise our child! Away from all of this!" She pleaded with him, hoping to get through him.

"Luke...", Padme uttered the name of their unborn son, wondering what could he had thought of his father after realizing who he was despite Obi-wan's words about him that motivated him to become like his father.

"Don't you see? We don't have to run away anymore! I have brought peace to the Galaxy! I'm more powerful than the Chancellor! I can overthrow him!" Anakin proclaimed in an effort to convince her.

"Of course, there is the Rule of Two", Master Tiin sighed to himself.

"And together we ran rule this Galaxy! Make things how we want them to be!" He continued, not before Padme began to take a few steps back away from him.

"She's seen through him...", Depa pointed out.

"This...isn't Skywalker anymore...", Mundi added, no longer finding any qualities that Anakin had to the Sith Lord they witnessed.

"I...I don't believe what I'm hearing Obi-Wan was right! You've changed!"

Anakin was already afraid of himself and he found the strength to call out. "Padme, whatever you're trying to do. You have to keave now..."

"I don't want to hear another word about Obi-Wan." Anakin warned her, wanting to dodge the subject.

"Do not provoke him, Senator", Mace equally warned, realizing his change of demeanor. "You are crossing dangerous borders"

"I don't know who you are..." she finally spoke, her eyes were already the verge of tears upon realizing who he truly was. "You're breaking my heart...you're going down a path I can't follow!"

"Because of Obi-Wan?" He said, his face carrying loss.

"Because of what you've done! Stop now! Come back! I love you!" She cried out, pleading with him but his eyes now glared at her with his fury.

"LIAR!" He screamed at her, all sense of passion replaced by sheer rage.

"Padme, get out of there now!", Anakin called out again, realizing the worst case scenario. And one he could not bear to imagine.

"What? What happened?" Ahsoka asked not knowing why her Master became suddenly enraged, especially towards his own wife.

Padme turned around and her blood ran cold. Obi-wan was on the ship. He must have been hiding in the cargo bay. She now knew Anakin thought she was betraying him. Obi-Wan walked slowly down the steps of her ship as Anakin's rage was growing.

"YOU'RE WITH HIM! YOU BROUGHT HIM HERE TO KILL ME!" He accused her, no longer caring what he had told her earlier.

"He had thought that Senator Amidala had brought Master Kenobi with her, but I don't think she knew that he had hidden on her ship", Depa pointed out.

He realized the volatility of the situation at hand. "No...no...DON'T YOU HURT HER!", Anakin warned his future as Rex and Ahsoka stood by him.

"No! Anakin I didn-" She was cut off as she saw him hold out his hand. A veil of red descended on the world. She clawed at her throat, but there was nothing her hands could touch.

"NOOO!! NO! PADME!", Anakin screamed in terror as the present Senator, Rex, Ahsoka and Obi-Wan restrained him from trying to stop his future from choking his pregnant wife, not risking the holoplayer to be damaged or destroyed.

The Senator only covered her mouth with both hands in terror, horrified at what he had done to her. And it didn't take long before she began to weep, realizing that the Anakin she knew was already gone. "Anakin, why?"

"LET HER GO ANAKIN!" Obi-Wan commanded in a rare moment of anger, stepping out of the ship.

Obi-wan and the rest of the Jedi were horrified at how much Anakin had fallen. All because of the order's flaws and of Sidious. "Anakin...why her?", Obi-Wan painfully asked to himself.

Anakin just continued to exert his power over this act. His anger was already blinding him to what he was doing.

"LET. HER. GO!" Obi-Wan repeated, jus as Anakin finally let up and Padme collapsed to the ground, unconscious.

"NO!", Anakin shouted with the strength his lungs could handle and he sank to his knees weeping at Padme's lap. "I'm sorry...I'm so sorry..."

Padme couldn't say anything as the holoplayer left her in sheer silence and terror on what is to come, but fresh tears continued to flow from her eyes, not bothering to wipe them due to the trauma inflicted on her.

"By the Force." Shaak Ti whispered covering her mouth, at the sight of Anakin harming his wife, the very person he sacrificed everything for.

"He..he killed Senator Amidala." Rex said, his hands trembling at the sight. Ahsoka felt helpless as she witnessed her friend's grave predicament in front of her.

"He killed his own wife." Windu said, disappointed at this act of blinded rage.

Obi-Wan knelt beside Padme's unconscious body, where she lay limp and broken in the smoky dusk. He felt for a pulse. It was thin, and erratic.

Looking away, the Sith Lord turned the turned his attention to Obi-Wan, his eyes blazing with combusted anger. "YOU TURNED HER AGAINST ME!"

"The slightest hint of betrayal is enough for him to see anyone as his enemy", Plo Koon uttered, horrified on how much the Dark Side had consumed Skywalker.

Ahsoka and Rex's eyes widened in fear and anguish, realizing that the man in front of them was not the same man who had cared for them over the years.

Obi-Wan looked at the best friend he had ever had, realizing he was too far gone. "You have done to yourself!", the Jedi Master shot back.

Pacing back and forth, Vader roared at him. "YOU WILL NOT TAKE HER FROM ME!"

"He's too far gone...", Shaak Ti admitted in complete reluctance, seeing that this was far from the war hero that she had fought alongside with. "Vader has taken over him"

"He is no longer the Jedi that we have all known...", Kit Fisto added in an equally harrowed tone.

"Your anger and lust for power have already done that", Obi-Wan somberly replied in a tone skin to that of a disappointed father, removing his cloak as he circled his former apprentice. "You have allowed this Dark Lord to twist your mind, until you have the become the very thing you swore to destroy!"

"Don't lecture me, Obi-Wan!", Vader spat. "I've seen through the lies of the Jedi! I do not fear the Dark Side as you do!"

"Turned him and others away from the light, we did", Yoda professed, seeing the truth in Anakin's words. "Flawed the order had become..."

"I have brought peace! Freedom! Justice! and security to my new Empire!", Vader proclaimed.

"YOU HAVE DONE NONE OF THOSE!", Anakin shouted angrily to his future, trying to accept what was running through his head. "AND YOU NEVER DID!"

Looking at whatever insanity that got through his head, Obi-Wan asked back. "YOUR new Empire?"

"He intends to overthrow Sidious once he learned what he can...", Mundi pieced out. "Just as Bane had in mind"

"Don't make me kill you", Vader warned him.

"Master Skywalker and Master Kenobi...are going to fight?", Caleb questioned in disbelief, as he had known the two of their brotherhood and qualities as a formidable duo.

"I wouldn't fight him...I would never", Anakin uttered in denial, desperately hoping that Obi-Wan could simply just take Padme away and run.

Obi-Wan couldn't believe what he was hearing, and he responded. "Anakin, my allegiance is to the Republic! TO DEMOCRACY!"

Vader conceded to his point and declared. "If you're not with me...then you're my enemy!"

"No...please no...anything but that", Padme begged, not wanting that the two wouldn't fight for all they have went through over the years.

Realizing there is little to be done, Obi-Wan closed his eyes in surrender. "Only a Sith deals with absolutes..", he answered back, drawing his lightsaber. "I will do what I must"

No...both Anakin and Obi-Wan thought to themselves, painfully realizing what will happen next.

Master...Master Kenobi...Ahsoka closed her eyes as she began to weep at what comes next. And she did not mind the comforting arm that Rex offered over her shoulder in an attempt to remind her she was not alone.

"The fate of the Galaxy is at hand...", Mundi marvelled the concurrent duels in hand.

"As we are the chosen few to have seen it", Master Fisto further added.

For Anakin, Obi-Wan, Padme, Rex and Ahsoka, they could only brace themselves of the pain that lies ahead.

The Dark Lord glanced behind him, Obi-Wan's eyes widened in terror when he saw the yellow orbs rather than the shining blue that once held the image of the Jedi Knight he had for a brother.

"You will try..."

The Sith Lord leapt towards the Jedi Master. Blue blades crossed, and the volcano above echoed their lightning with a shout of fire.


AN: Stopping here now! And I could imagine people raising pitchforks and torches demanding when will be the next.My reply? I'll never tell. (Muahahahahah!) Leave a review and speak your thoughts of the chapter! would totally appreciate it!