Part 1

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Wind blew through the city streets, threatening to blow Percy off the roof as he explained the situation to Chief Oran. "Sonic's operating system is shut down, but his friends took him away."

Oran nodded. "Well, we'll have to fix that later. But in the meantime...well done Percy!" A beaming smile crossed his face.

Percy shook his head. "But sir, Sonic wasn't captured. We can't reprogram him."

"True. But his systems are shut down. He won't be a threat anymore. And that's the important thing for now. It's nice to finally have some good news." Oran turned to face the streets below. "Besides. We know where he's headed. And Metal Sonic is operational again." Oran looked at Metal Sonic as it ran through the streets. It scanned its own systems checking to make sure everything was operating correctly. There were no errors detected.

The sensors ran across the ground and buildings. So far, all detected life forms were human and animal non-variant. None showed significant levels of chaos energy like that in Knuckles, Sonic, or Shadow, but the destination site hadn't been reached yet.

Soon Metal Sonic came to the entrance of the water treatment plant. The robot's parameters demanded that no damage could be done to the treatment plant, and keeping the water safe was the top priority. Secondary priority was recovery of Sonic, followed by capture of any other supernatural animals.

The black streets and metal skyscrapers gave way to smaller buildings, and eventually a concrete canal with a flowing river. Metal Sonic followed the river to a tunnel, entering at top speed. As visible light disappeared, Metal Sonic's systems started sending out small sounds to tell its surroundings by radar. A map of the tunnel system formed in it's database to update the information it already had, but there was still no sign of any life forms. There weren't any detectable sources of electricity or energy nearby either. Soon, Metal Sonic got far enough into the tunnels that it's communication with headquarters was cut off. It could no longer receive orders or send data back. From here on out, it was on its own.

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Part 2

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Knuckles and Amy collapsed to the ground as they finally met up with Tails, who had been working on a laptop. It sat on a metal lit by battery powered lamps. Tails looked at Sonic, who still had a heartbeat and was breathing, but didn't react to his name. "Hey Sonic! Sonic! Wake up!"

"He's not getting up." Knuckles heaved between gasped breaths. "Whatever that EMP did to him, it wasn't good."

Tails struggle to lift Sonic onto a metal table surrounded by tools. After visiting the landfill he'd found enough machinery and scrap metal to make a pretty good workshop. He took out a device to check Sonic's systems. It didn't look like any wiring had been fried. For that matter, there didn't even seem to be any damage throughout his entire body. "Huh, that's odd." He kept looking over Sonic's systems.

Amy sat up, managing to somewhat catch her breath. She looked at Tails. "What?"

Tails kept looking over Sonic. "Well...I don't see any damage to Sonic. The organic parts don't seem to have any issues, and neither do his robotic parts. Maybe I'm missing something, but from what I'm seeing, Sonic's fine. So it kind of bugs me that he's not waking up."

Amy thought for a moment. "Well, he did say he'd need some time in the sun to recharge his super speed. Maybe he just ran out of power?"

Tails shook his head. "No, that's not it. He's at well over half power, so he should definitely be able to move around right now." He looked at Sonic's head, there was a latch at the top that looked fairly easy to open. "I wonder…"

Knuckles sat up, a concerning thought came to him. "Tails, you don't think that EMP messed with his brain do you?"

Tails took a scan of Sonic's brain, then shook his head. "No, he's not malfunctioning, and his brain's definitely fine. I don't think that EMP did any real damage. It's almost like he's been turned off, like it's something his systems were meant to do."

"What?" Amy stood up, walking over to Tails. "That doesn't make any sense. You can't just turn someone off." She shook her head. "This is one weird hallucination."

Tails raised an eyebrow at her, then shrugged. "Sonic's part robot, so it makes sense. And on the plus side it means he's not in any danger. Once he turn him on again, he should be fine." He thought about popping the lid on Sonic's head, but stopped. "Problem is, I don't know how to do that, and if I mess up, there's no telling what it'll do to him."

Knuckles sighed. "Well, at least we know he won't die on us. Any idea how it'll take to figure his systems out."

"I'm not really sure. It'll probably take me at least a week, but I doubt it'll take me more than a month. Still, it's hard to say. I'm not really familiar with his design systems. The only thing I have to go on is his coding. I'm just glad I know the programming language already, matlab might be a pain, but at least it works for robotics." Tails' smile faded. "But I don't know how I have to wake Sonic up. Even with his low metabolism, there's a real risk of him dying of thirst or hunger."

Knuckles grimaced. "He might deserve it, but we can't afford for him to die." He looked around the workshop. "I know this is a little sudden, but we should probably get out of here as soon as possible. Do you have any way to move your tools out from here?"

Tails clicked a button. "Yeah. Figured we might need to move. I managed to rebuild some remote control cars people threw away." Several carts came into view. Tails started shoving tools into the carts. "I can get these to follow us anywhere we go."

"Whoa." Knuckles looked at the machines in amazement. "Kid, you're something else."

Tails scratched the back of his head laughing. "Thanks." Then his eyes narrowed at a sound coming down the tunnel. "Hey. Did you guys hear that?"

Knuckles and Amy both nodded. "Yeah." Knuckles turned toward the sound. "You guys wait here. I'm gonna check that out."

Sweat formed on Amy's forehead. "Hey Tails. You wouldn't happen to have my hammer would you?"

Tails shook his head. "Sorry. None of the files I managed to get said anything about your hammer. I have no idea where that might be."

"Yeah I figured." Amy dropped her shoulders. Then she noticed a long pipe like piece of scrap metal in one of Tails' carts. "Hey, you mind if I borrow that?" She pointed at the scrap metal.

Tails pulled out the scrap metal. 'This? Sure." He tossed it to Amy. "Take this too." He threw Amy a construction helmet with a headlamp on it.

She caught both objects, putting the helmet on. Then she felt the metal in her hands. Not quite like her hammer, but the weight and momentum were close enough. "Thanks. I'm gonna go check on Knuckles. I have a feeling those soldiers are catching up to us."

Tails pushed a button on Sonic's metal table. Wheels popped out at the bottom as Tails pulled some belts to strap Sonic to the table. "Then get Knuckles, and we'll ride my carts out."

Amy nodded before running after Knuckles. Then she heard a yell from Knuckles. "Ahhh!" The sound echoed through the tunnel as Amy got closer and closer. Then she saw him. "Knuckles!" Knuckles was still standing, but his right shoulder had swelled into a purple balloon. Blood dripped from his mouth as he faced off against what looked like a robotic version of Sonic, its eyes glowing red. A small tear in it's armor showed blue sparks of electricity.

The robot turned to face Amy, and Knuckles threw a left hook. The robot dodged, and threw Knuckles into the wall. It went to ram him, but Amy smacked it away with her metal rod. The rod bent, but the robot had a dent to match, right on its head. Amy felt the vibration through her hands, barely able to hold onto the rod. As the robot recovered, it charged Amy with its wheels screeching.

She aimed her rod, throwing it like a javelin. The rod hit the robot, shattering as shrapnel flew across the tunnel. For a few seconds, Amy couldn't see anything. There was nothing but silence. Then she was able to see the robot. It wasn't moving, a gaping hole in its chest, and its eyes gone dark. Amy grabbed Knuckles and helped him stand. "Come on. Let's get out of here."

Knuckles gave a grunt, but nothing else. Then Amy put him on her shoulder, running after Tails.

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Part 3

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Dr. Robotnick looked over a file on Sonic's code. He hadn't considered it before, but he should probably have a system in place to immediately reprogram Sonic on retrieval. That fox child had already managed to hack into the security system. He might be able to restart Sonic too. After all, the fail safe was never designed to kill Sonic. That would raise too many questions. He had to make sure Sonic wouldn't hurt anyone. Still, something felt wrong as he coded Sonic's new program. Sonic was part robot certainly, but he wasn't just that. Reprograming Metal Sonic was one thing, it was just a machine, but Sonic was alive. Was it right to take away someone's free will, even if they were threatening others?

He sighed, trying not to think about it too much. Robotnick turned to his assisstant James as he worked on an increased range for Sonic's failsafe. "What's your current estimate for the fail safe's maximum distance?"

James turned to Robotnick. "Well, there are two designs that I have right now. One will take about two weeks to build, and has a range with a radius of 2 kilometers. The other is twice as expensive and will take about a month to build, but has a range with a radius of 20 kilometers. They also can send a constant signal, but aren't portable."

Robotnick nodded, taking a sip of coffee. "That should at least keep him from causing any trouble in the city." He sighed. "It's sad that it's come to this. I wish there was another way."

"Traitor's brought this upon himself. We're just defending ourselves and the city." James looked over the designs to the two fail safes. Both showed blue outlines of a sattelite dish against a black background. He looked at the design. "Hopefully Metal Sonic can bring him in. I'd rather not take up too much of the police budget."

Robotnick kept looking through Sonic's code, making edits where he thought it made sense. Then he came across that made him hesistate. He could add a set of command codes that would routinely erase any thoughts and memories that would make Sonic turn against Chaos Control. He'd already written the coding along time ago, but he hadn't added it to Sonic's systems. He weighed his options, but even after a few minutes of thought, he still couldn't decide what to do. He moved on to other parts of the code, as he kept thinking about the command codes.

He kept working and thinking. Then an idea came to him, a clone. If he could grow a clone with Sonic's memories up until that child died. What was her name again, Cream? Robotnick had suspected that had messed with Sonic, he wasn't the same after, and the changes showed strongest right before he went rogue. There had to be a connection. Maybe he could make a new code that could just keep him from remembering events of that magnitude. Designing a code with that much detail would take, so he'd have to focus on that for a while. Then he'd focus on an internal kill code, one that would shut him down if his loyalties ever changed. Back when he'd first built Sonic it didn't seem necessary, now he knew better. Whatever it took to protect the city, he would do it. As he worked on the code, a dull pain filled his heart. His stomach turned thinking about what he was doing, and tears started forming on his eyes.

A single whimper came from Dr. Robotnick before he managed to force his mouth shut. James turned to him to see the tears in his eyes. "Hey, what's up Doc? You get something in you eyes?"

Robotnick shook his head, trying to keep his voice level. "It doesn't matter. I've already made up my mind to go through with it." His voice dropped to a whisper. "I'm sorry Sonic..."

James looked at the old roboticist. He couldn't tear his eyes away from the Robotnick's shivers. "I'd tell you it's for the greater good, but I doubt that'd help. I'm sorry you're the only one who knows his code well enough to do this. I can't imagine what it'd be like to hurt anyone in my family."

"343's not family." Robotnick gritted his teeth, trying to ignore the pit in his stomach.

"Yeah he is." James truned back to the designs. "What else do you call someone you raised from birth?"