Whisper was walking through part of the city, she went past Akhlut being taken away. A gunship lands in front of her, it opens to reveal Amy, Fang and an unconscious tied up Scourge. Whisper smiled "You actually captured him. I'm impressed" "That is what the council wanted" Amy said blankly. The two walked together "Still. You succeeded where many have failed" "I've learned from the best, including you". Whisper sighed "I wish I was good at something other than war". She looked out to a destroyed part of the city; Amy gave her a reassuring smile "Your people need a new kind of leader". Whisper paused "My sister tried that. I never understood her idealism". Fang came up to them "Commander. I have the council waiting" "And Master Shadow? Were you able to contact him?". Fang nodded "He was at the meeting when I left to get you", Amy turned to Whisper "Go. I can handle things here".
Inside a portable command centre, holograms of Council members were talking. Merlin stared intently "I sense a plot to destroy the Shinobi. I feel the dark side surrounding the Chancellor". Nate pondered "If he doesn't give up his emergency powers after the destruction of Dark Oak then he should be removed from office". Merlin nodded "The Shinobi Council will have to take control of the Senate in order to secure a peaceful transition". Blaze looked troubled by these words "We must take great care with what shall be done next". Amy entered and Merlin turned to her "I understand your mission was a success". Amy nodded "Yes. I have Scourge in custody. I will escort Commander Fang when he delivers him to Mobotropolis". Blaze smiled "You have done a great service to the Republic" "I did my duty as a citizen". Blaze face dropped slightly "Not as a Shinobi?". Amy shook her head "No. Not yet. Actually, I was hoping to speak with General Shadow" "I sent him to inform the Chancellor that Dark Oak has indeed been located on Mova" Merlin answered. Blaze nodded "Yes. Master Espio has engaged him" she added. Amy looked hopeful "Then the war could be over soon" "That depends on the Chancellor" Merlin said. The Council members stared at each other, confusing Amy "What do you mean?" "I'm sorry, citizen. These matters are for the council to discuss" Merlin said coldly. Amy hid her irritation "I understand" all the council left except for Blaze "Amy. You have more to say? A message for Shadow, perhaps?". Amy thought of what to say but gave up "No, Master. Thank you. I'll tell him myself when I see him". Blaze nodded "May the Force be with you, apprentice" she cut off. Fang stepped closer to Amy "You didn't tell them what Scourge said about General Shadow" "No, I didn't".
A new cruiser arrived and dropped off a small battalion of the Mobotropolis guard clones on the planet to help escort Scourge. On the docking bay a group of clones were standing on the left side of the entrance while masked Wispons were standing on the right. Amy and Fang watched as the doors opened, Whisper and Claire came through with what looked to be a metal sarcophagus being pushed behind them. They got closer and Amy saw that it was a capsule with a small glass window. Inside was Scourge with his mouth covered, they could hear him breathing heavily and saw pure rage in his eyes. Fang and the Mobotropolis guard led the capsule inside a personnel carrier that a shuttle was attached to. Amy smirked "Impressive. I doubt even Scourge could get out of there". Whisper stood next to her "A relic of a bygone era, when Wispons had a reason to imprison you Force-wielding maniacs" "I thought your sister outlawed such devices". Whisper smiled "She did. This is the last one". She turned to Amy and they happily shook hands "Goodbye, Amy Rose". Amy nodded and went inside the carrier. The shuttle then took off carrying it and headed for the Republic cruiser in orbit. Inside the carrier, Scourge was silently watching Amy and the clones before closing his eyes and listening through the Force.
The shuttle landed in the hanger, Fang and Amy led the capsule out of the carrier, the guards took him from there and took him to a reinforced cell. Amy and Fang headed to the bridge, once they entered the whole crew saluted Amy. They both walked up to the window and watched as the cruiser jumped to hyperspace. Fang noticed Amy had been silent for a while "Something on your mind?". Amy paused before answering "As a Shinobi, we were trained to be keepers of the peace, not soldiers. But all I've been since I was a youngling is a soldier". Fang could relate to that "Well, I've known no other way. None of us have. Gives us clones all a mixed feeling about the war. Many people wish it never happened. But without it, we clones wouldn't exist". Amy smiled "Well, then perhaps some good has come from all of it. The Republic couldn't have asked for better soldiers, nor I, a better friend". She saluted him which he happily returned. A snake clone walked over to them "Commander Fang, the latest briefing has come in from Mobotropolis". Fang looked to Amy "Want to have a look? It might have an update on General Espio's efforts" "You go. I'm sure it's more good news". Fang nodded and headed into the next room; Amy turned back to the window.
Inside a cell, Scourge was still inside the capsule. He heard a lightsaber ignite causing him to open his eyes which were now full of fear "You must choose". Amy began to hear the voices as well "He has control over the entire Senate" "Master, he must live" "He's to dangerous to be left alive" she recognised the voice. The voices got louder "Please don't!" "I need him!". Amy clutched her head as she felt unbalanced, she could hear screams of pain and then "UNLIMITED POWER!". It suddenly went silent and then "What have I done" there was great fear and guilt in the voice "Shadow?" Amy said. In the next room Fang was standing in front of the holo-unit which was showing Mephiles he stared at him confused when he spoke "Execute Order 06", Fang nodded "Yes, Lord Mephiles". The hologram cut off, Fang took off his hat, leaned against the unit and began to breath heavily as if in pain. Amy ran inside "Fang. It's Shadow. I feel like something terrible has happened". Fang stood up straight and dropped his hat on the ground, his hands started to shake "Fang?". The commlinks on the two clones behind Amy activated and she heard a voice. The two clones then turned to her and raised their blasters with expressionless faces. "No! I'll do it" Fang said as he turned to her with a pained expression on his face. "Fang, what's happening?" she too a step forward but Fang raised his pistols "Stay back!" his hands were trembling.
Amy raised her hands and stared at Fang looking betrayed. Fang's face began to shake as tears formed I his eyes "Find him". He closed his eyes and struggled to speak "Find him. Mighty. Find him! Mighty!" he fired but Amy quickly dodged. She ran towards him and pushed him onto the holo-unit. She used the Force to shut the doors to the bridge cutting off the two other clones from them. She ignited her lightsabers "Fang!". Jet along with a squad of clones entered and fired on Amy. She deflected the blasts upwards creating smoke around her along with weakening the roof. She then jumped up and the clones couldn't see her "She's down. She's down" "Hold you fire! We got her!". The smoke cleared and she was gone, they noticed a large hole above the unit. "Sir, are you alright?" an Orca clone asked helping up Fang who was clutching his head "Fine, just tired is all" he picked up his hat and put it back on. "I want you to go to the detention level. Execute Scourge", the orca and another clone exited the room. Fang looked to the rest of the clones with a blank expression "Alright. We know Amy Rose is on board. She's been marked for termination by Order 06. Under this directive, any and all Shinobi leadership must be executed for treason against the Republic". All the clones including Jet listened with cold expression "Any soldier that does not comply with the order will also be executed for treason. Understood?" "Yes, sir!" they all said. Fang nodded "There are only so many places to hide on this ship. Gather up search parties. We'll fan out and move section by section. Let's get moving". All the clones ran out of the room, Fang picked up his blasters and walked out with them.
Scourge was staring out of his capsule as two clones entered. Scourge tried to struggle against his restraints as the clones opened the capsule and raised their weapons. He then looked behind them and saw Amy at the cell door. She quickly threw one clone to the wall with the Force, knocking them out. He charged at the other one, cut his blaster in half and knocked him to the ground. She raised her lightsabers near Scourge's face "Don't make me regret this" she cut through his restraints. He fell to his knees. He coughed "You- You survived", Amy glared down at him "Is this your doing? Choose your words carefully" she put the lightsaber to her throat. Scourge shook his head "No, no. This wasn't me. I don't know what's happened, but surely, you've felt it. The voices crying out. The death". Amy stepped back "The clones turned against me. Even Fang. I don't know why; they just suddenly weren't themselves". Scourge started to chuckle "Brilliant. Brilliant. I didn't know my master's plan, but now, now I see it. He turned the Shinobi's own army against them". He stood up "You've done the right thing by coming to me. Only together can we survive this. Now, if you will follow my lead". Amy put her lightsaber to him "You don't understand. I'm not here to team up with you. I need a diversion, and you're it. Now go cause some chaos. It's what you're good at". They both stepped out of the cell "Uh, can you at east give me a fighting chance?" he held out his hand expecting a lightsaber, "I'm not rooting for you. Now get going". Scourge scowled at her before going off in the other direction.
Fang was walking through the halls of the ship when a patrol ran up to him "Sir, we've finished our sweep of the detention level. The prisoner has escaped. There's no sign of Rose or Scourge". "Destroy the escape pods and increase security on the hanger. Orders say if the Shinobi escapes then we destroy all shifting inhibitors onboard the ship" "Yes, sir".
Amy entered a compartment room with three gizoids inside. She recognised one of them and activated it, it beeped "Shh. Charyb, I need your help". Charyb started beeping in a panicked fashion "I know. I know. Be quite" the lights turned on along with the other gizoids. They all started beeping "I don't know. I don't know why the clones are doing this. But we might be able to do something about it. Are you sure you wanna help? It could be dangerous" they happily beeped. Amy nodded "Okay, let's get started. Charyb, patch into the central computer. Bring up every secure file on CT-06-1993" the gizoid plugged into a computer console and projected a hologram of Mighty's file before showing a recording of Elise. "An independent investigation confirmed that CT-06-1993 experienced a malfunction with his inhibitor chip. Both the Senate committee and the Shinobi Council have accepted these findings. However, a grievance report was filed by CT-1994". Amy pondered "Charyb, bring up that report". Charyb beeped "Try Shadow's pass code 0-6-0-1". Charyb then showed a hologram of Fang "I already know this report's gonna fall on deaf ears, but I owe it to Mighty to record what I saw. I'm not sure I believe it myself but there's a possibility that the inhibitor chips the Soleannans put inside us have a purpose that we don't yet fully understand".
A group of clones were backing up while firing down a corridor "Fall back! Fall back!". Scourge walked round a corner and glared at them as he kept advancing. He pulled a plate of metal off the wall and used it as cover from blaster fire. He kept walking and threw one of the clones up against the ceiling before throwing him back down. He throws the plate at two other clones, removing their heads. He grabbed two more plates which hit two clones before he started using them as cover. He threw one of them at Big the Cat, it hit him in the stomach killing him. The remaining clones kept backing up while one got on his commlink "Big's down! Scourge's advancing toward the main hanger" "You must seal the blast doors. Stop his advance!". Two of the clones ran ahead and pressed the button to close the door while a beetle clone was giving them cover. Once the doors started closing the beetle clone ran through but suddenly his right arm was getting pulled back. He looked around and saw Scourge holding out his hand. The two other clones grabbed their brother trying to save him, but his arm passed the doors and he started to scream as the doors closed around it. It finally closed, severing the arm which fell to the floor. Scourge stepped up to it and heard the commlink on it activate "Trooper, did you seal the doors? Trooper? If you read this, seal the door. We want to redirect his approach. Over".
Fang was running through the halls of the cruiser when Charyb stepped in front of him "Hey, hey. Out of the way!" he said angrily. The two other gizoids ran out and closed all the doors around Fang, separating him form the other troopers. Fang stared at the gizoids confused "Are you crossed-wired?". Charyb projected a hologram of Amy which Fang stared coldly at "Fang. I think I know what's happening. I saw your report on Mighty". Fang's eyes shifted slightly when he heard the name "It isn't your fault. You were programmed. Your mind was altered to do this when you were very young. I can help you". The message ended and Fang angrily pointed his pistol at Charyb who backed away scared "Where is she?" "I'm right here". Fang turned around and saw Amy but Charyb then came up behind him and shocked him with his hand. Fang screamed and fell to the floor unconscious. Amy heard the other clones form behind the door "Cheep, are all the doors sealed, so the way is clear?". The red gizoid nodded "Okay. Let's get him to the medical bay". The three gizoids carried Fang and they started running down an empty corridor.
They entered the medical bay and placed Fang on an examination table, Amy took off his hat "Charyb, run a scan. See if you can find the inhibitor chip the report talked about". A medical bot stepped towards the table and scanned Fang. Amy heard the clones on the other side of the door "G-G, if they override the door controls you have to reseal it fast" G-G ran over to the door controls. Amy saw on the screen that the chip was in his head, she ran over to a cupboard, but it was empty "What? Where are the inhibitors?". The medical robot beeped "What? We can't get the chip out without it". Amy thought for a moment before going next to Fang's body and placing her hands on his head. She closed her eyes "I am one with the Force and the Force is with me. I am one with the Force and the Force is with me". Fang started saying the same thing and they were now saying it together "I am one with the Force and the Force is with me". Amy concentrated and was able to tell where to get the chip while Fang was in this form. Amy went over to the screen and directed the medical bot on where to cut. The robot got to work as Amy heard the door getting forced open. She ignited her lightsaber "G-G, get ready on the door". The door opened and clones started firing inside. She deflected the blasts and pushed them back, but she was getting overwhelmed by the rate of fire. She dropped one of her lightsaber and was barley keeping up with the blasts "The door! G-G, the door!". Suddenly, blaster bolts came from behind Amy and shot the a few of the clones before the door finally closed. Amy turned around and saw Fang, conscious with a patch over the right side of his head. He was holding his pistols up and looked horrified but what he had just done, "Fang? Are you okay?". He lowered his pistols "Yeah. Yeah, kid. I'm okay. I'm…. I'm sorry for what happened earlier. I… I almost killed you". He put his hand over where the chip was cut out. Amy stood in front of him "How widespread is this?" "Amy, it's all of us. The entire Grand Army of the Republic has been ordered to hunt down and destroy the Shinobi Knights".