Disclaimer: I own nothing and make no money off this story. All rights go to Lucasfilms. Hope you enjoy my twist on this story.
The Liberty, Bridge
Although Aayla Secura was not a member of the Jedi Council, Master Windu entrusted the secret of the plot to her and she knew exactly which one of her troopers to trust with this information. That very Trooper walked onto the Bridge and met with his General. Aayla fixed her gaze and said, "Commander Bly it is good to see you." Bly smiled under his helmet and said "Reporting as ordered General." Aayla smiled at his rigidity and said "Bly there is no one here. There is no need for formalities." Bly relaxed and removed his helmet. He had a small smile on his face and walked over to his General before he pulled her in for a kiss. Aayla reciprocated and deepened it. This relationship was very new and both individuals were trying to take it slow. Although, it was hard sometimes.
Several Months Ago
The Liberty, Aayla Secura's Private Chambers
A few months ago Bly had come to Aayla's private chambers and asked to speak to her. He admitted that although he had only known her for 2 years, he had realized that he loved her. She cared about the troopers under her command and she had saved all of them more times than they could count. She wasn't cold and callous like the Kaminoans were. She was warm and bright. She had an aura of love and respect for all those around her. Of course, her beauty was a major plus as well. Aayla was unsure what to say, she had felt the beginnings of romantic feelings for the commander as well and was unsure how to proceed.
Master Yoda's Private Council Room, Jedi Temple
She confided in Master Yoda and was honest about all of her feelings. To her surprise, Yoda would allow a relationship to take place. He explained that relationships were forbidden because a Jedi needed to be clear-headed and not let emotions cloud judgment. Although, in some cases, the desire to protect loved ones made certain Jedi better versions of themselves. One example he gave was Jedi Master Ki-Adi-Mundi. He had a wife and a child. His family did not cloud his judgment and he became closer to the force because of the love his family shared. Aayla was happy and thanked her Master for understanding.
The Liberty, Bridge
After they separated Aayla smiled at her lover and said "Tonight I'm taking charge." Then her expression grew serious. "However, I did have something important to discuss with you." Bly dropped his smile and gave her his full attention. She sighed and said, "The Jedi Council has discovered a plot to not only wipe out all the Jedi but to tear apart the republic from the inside." Similar to Wolffe, Bly's face paled as he remembered the carnage of General Krell and the report submitted by Captain Rex. Aayla noticed his face and continued "The incident involving Clone Trooper Tup and Arc Trooper Fives revolved around their inhibitor chips." Bly nodded remembering the official report and conclusion but knew that this conversation was far from over.
Aayla continued "Unhappy with the investigation Captain Rex and Lieutenant Jesse of the 501st removed their chips as well." Before she could continue, Bly interrupted and asked "What happened? Did they try to hurt any Jedi? Did they go nuts?" Aayla raised a hand to calm him before she responded "No there were no adverse effects at all. That's the strange thing. If the chips were vital and made you behave in a normal fashion then they should have gone mad the moment they were removed but nothing happened. Stunned by this they decided to scan the chips and came upon a frightening discovery. There are a number of contingency orders implanted in each chip. These orders have various technicalities but one order sticks out. It is Order 66. Essentially it says that if the Jedi ever act in a way that is not aligned with the Republic's interest then the GAR, with special orders from the Chancellor, is to execute them immediately and the Chancellor will take control of the GAR.
The chips were either manipulated or made by a Sith." Bly knew what the Sith were, more than other troopers. His relationship with Aayla included learning all about her religion and the machinations of the Sith. Aayla continued on "The way Order 66 is stated, implies that the Chancellor is heavily involved in this plot to destroy the Jedi and the Republic. The Jedi Council met and they told us to find certain troopers under our command who we trusted completely. Naturally, I chose you. We must begin removing these chips as quickly as possible. From the way Tup acted, if this order activates no clone will have a choice. It will not be something you can control. I can't stand the thought of any troopers being programmed or forced to do anything. You may be clones but you are living beings. You have hearts, souls, and you are all connected to the force. I will not allow any Trooper, especially those closest to me, to be treated like droids."
Bly smiled and gave his lover a warm hug, which she returned. Bly looked into her eyes and said "Thank you, General, your care for Clones and especially those under your command always leaves me speechless. Thank you for telling me about that damn chip. I would never want to hurt you. In a few short months, you have become a large part of my heart and you have given me and my troopers a chance to live as free men; instead of just cogs in a war machine. I will remove my chip post haste. What do I tell the medical droid to look for?" Aayla shared a smile with her Commander before replying "Tell the droid to perform a Phase 5 Atomic level brain scan. Then tell it to remove any tissue foreign to the body. I will be down in a few minutes and stay by your side. I will make sure my face is the first you see when you wake up."
Bly smiled warmly and said "Thank you Aayla, I would like that. After I have recovered we need to come up with a way to remove the other chips from our Legion. Is there a way to do that without raising suspicion?" Aayla looked at her lover with a slight frown "I will not lie to my men. They have fought with me, bled with me, and in some unfortunate cases died for the Republic. They deserve to know the truth and they deserve to be free of that chips control. If they choose to side with the Chancellor I will not kill them but we might have to lock them in the cells until this mess is over."
While Bly didn't like the idea of locking his brothers up he understood it was better than lying to them about a situation this serious. Once again he was blown away by the care Aayla showed for the troopers under her command. She took no pleasure in locking them up if she had to but she would die before she allowed millions of innocent people to die and allowed billions of innocent people to be ruled by a ruthless dictator. That was one of the many things Bly shared with his General. He would lay down his life if it helped free people from an evil he couldn't well imagine. With that last thought, he walked over and gave Aayla a small kiss on the forehead, and walked to the medical bay knowing his love would be with him soon enough.
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