At last! I was so excited to finally get to this part of the story, mainly because I want to get on with the rest of the plot (and believe me, there's a lot of plot). This is perhaps the biggest chapter so far, so I hope you're ready to get comfy because lots of stuff is going down!

WARNING (and mild spoilers): Someone dies this chapter. Not saying who (if I told you, that would be a major spoiler), but if you don't want to read the details, then start skipping after the dialogue starting with "Yes... and no" and continue reading at the dialogue that starts with "Y-you killed him!" Thanks!

Now, without further ado, enjoy the many twists this chapter has to offer!

Project: Chaos Control

Chapter 5

Once the flash of light faded, Shadow the Hedgehog finally allowed himself an exhale of relief. Behind him, the younger two Supers let go of each other and took in their new surroundings.

Their refuge was dark and poorly lit, with patches of blue-white light coming from the overhead lightbulbs. The black and red leader turned to the wall behind him and after a short time of feeling the surface flipped a switch.

Instantly, the room became bathed in warm light. It appeared they had Chaos Controlled into a main computer room, the multiple screens blank for the moment.

Shadow walked up to the lone console.

"Where are we?" Silver asked, a slight nervous wobble in his voice.

"We're currently in one of many secret bunkers," Shadow replied, starting up the computer. With a small whirring sound, the machine came to life, displaying a loading screen in the shape of…

"Isn't that Eggman's logo?" Blaze questioned, alarm flashing through her pelt. Silver, realizing the same fact, glanced around them, expecting some sort of sudden attack. Instead, a monotone female voice responded.

"Scanning life forms… Welcome, Shadow the Hedgehog. Salutations, Silver the Hedgehog and Princess Blaze the Cat."

"E.V.E., restart all security programs and defenses. Block all contact attempts by GUN and activate all forms of cloaking."

"Acknowledged. Defenses online."

With a barely discernible hum, warm light flooded the room and the rest of the abandoned base, serving to welcome its new inhabitants. Security cameras came online once more, their recordings now displayed throughout some of the screens. The threesome watched as hallways, storage rooms, a small clinic, and even the battered remains of a robot factory finally saw the light. Dust was everywhere, but it might as well be nonexistent in the eyes of the three who sought a sanctuary-and found it.

Silver and Blaze shared a relieved and proud glance before turning to Shadow. The Ultimate Lifeform stood hunched over the control panel, allowing himself a small moment of grief over his failure to save Sonic, before pulling up a chair and seating himself.

"We're not out of danger yet," he stated simply. "We may have a safe place to stay for now, but I am willing to bet the Doctor didn't plan on ever returning to this place. We won't do ourselves any good leaving for supplies without some sort of cloaking device, but neither is rotting here with nothing a good idea."

Silver knitted his brow, at a loss for what to suggest to solve their new dilemma. Blaze, as well, couldn't think of any solutions.

Then, a four-note ringtone filled the silence and EVE's robotic voice provided the answer to its question.

"Incoming call from unknown source. Signal coming from: Tails' Workshop. Would you like to take it?"

"Yes," Shadow answered, mildly surprised that the young genius had figured out where they were hiding so fast. Static flickered on the main screen, but was soon replaced by the face of a yellow fox with sky blue eyes.

"Hello? Shadow?"

"Tails," the Ultimate Lifeform spoke. "How did you find us?"

"Well," Tails scratched the back of his head shyly. "Rouge told me about the secret bunkers and I've been calling each one for the last half-hour using the Miles Electric. Is everyone alright? Where's Sonic?"

Shadow clenched his fists and gritted his teeth, not daring to look the young fox in the eyes. "I was too late. GUN has him."

Tails blinked, trying to hold back the sudden wave of tears that threatened to fall. Sniffling, he tried not to dwell on the news and his brother's possible fate as he remembered why he was calling them.

"Shadow, Rouge wanted me to tell you something important. Turn on the news."

...

Sonic faced the GUN commander with his trademark confidence, successfully hiding the anxiety that threatened to break through to his supposed enemy. He hopped down from the bench, waiting for something to happen. Instead, Commander Tower glanced away from the speedy blue hero.

"I trust you will come quietly, unlike certain others?"

Sonic gritted his teeth, knowing who the "certain other" the Commander was referring to.

"You never had to hurt him like that," he stated, glaring at the soldiers. Some returned his gaze, unrepentant, while others looked away.

"Unfortunately, it was necessary for the sake of the project," Tower replied smoothly. "Besides, we can both acknowledge that power over time should never be left in the hands of any one person, especially one like him."

Sonic winced slightly at the sting of that last remark, even if it hadn't been aimed at him. Is that what the Commander thinks about the rest of us? Too powerful to be left alone?

The older human turned to two to the soldiers and nodded. Wordlessly, they entered the cell and made their way towards the trapped hedgehog with handcuffs at the ready.

Sonic stepped back threateningly. "Aw, Hell no. You're not putting those on me again."

"Sonic," Tower warned.

"No! Let me walk, at least, please?" the blue blur pleaded.

There was a moment of silence before Tower gave his reply. "If we do this, do you promise you won't try to escape?"

The speedy blue hedgehog gave him his trademark smirk and a thumbs up. "Heh, no problem."

"Very well," the Commander turned to the soldiers. "Just his hands."

The two nodded and complied, securing the hedgehog's hands behind him and unlocking his tether before guiding him to the door. The rest of the soldiers instantly snapped to formation, positioning themselves so that the world's hero was surrounded on all sides. Commander Tower stood at the head of the escort as they started down the hallway and towards the elevator.

Sonic glanced at the cell door next to his own, glaring at the plexiglass window just a head taller than him. He was sure Mephiles had heard the entire conversation. Whether the shade was gloating over his coming trial or still talking to himself was uncertain.

They continued the procession in silence, something that disturbed Sonic greatly and did nothing to ease the anxiety in his chest. And so, he decided to do something about that.

"So, what's gonna happen next?"

The GUN commander hesitated as he pressed the elevator button, wondering if he was authorized to give any information, then decided to uncharacteristically screw protocol and answer the hero's inquiry.

"First, we're taking you to the lab to have some of your Chaos Energy removed, alter its nature to act as an inhibitor, then return it. After that, you will stay here for a few days to recover, as the process does inflicts some pain, and then you will be released."

Sonic and the rest of the escort entered the open elevator. The Blue Blur was glad he had managed to pry some new information out of the otherwise tight-lipped commander, but something still bothered him. "But why inhibit my Chaos Energy?"

Tower sighed, not liking what he was about to say. "According to my superiors, it is to control powerful individuals. But according to my own observations, it is to destroy the Super form."

...

Shadow found himself staring in amazement at what was happening on the news, a hand to his head as he tried to take in what was going on.

All around the world, people were protesting against the announcement of the new initiative Project: Chaos Control. Some raised signs denouncing GUN, some blocked whole freeways, and a few others dared to burn the GUN flag.

Some familiar faces, including Amy, Omega, and even the Babylon Rogues could be seen often among the sea of protesters, declaring their support for the persecuted.

All three of the Supers stared, barely registering that this was actually happening. They were frozen in shock and awe.

Finally, Shadow snapped out of his trance and stood, resolve hardening his features.

"We can't let this opportunity go to waste," he said, turning to the younger two. "They're protesting for us, they're fighting because they believe we are heroes. We need to take advantage."

The Ultimate Lifeform whipped his head back to the computer. "EVE, are the cameras online?"

"Yes, Shadow," the A.I. answered.

"Good. Hack into all news broadcasting frequencies. Record whatever I say."

...

Once the elevator doors opened, Sonic squinted his eyes at the sudden brightness of the lab. All of the scientists turned at their arrival, standing in respectful silence at their subject.

Commander Tower waited a moment, then stepped into the room, Sonic and the rest of the escort following suit. The stares of the human scientists only made the blue hedgehog even more anxious, and so turned to the Commander.

"So, we Supers are too powerful to be left alone?"

"Yes, according to my superiors," the older human replied. "They feel threatened by the amount of power you and your friends possess, and don't want to risk leaving the power with you when you could easily wipe out continents."

"But we're heroes!" Sonic protested, frustration clearly evident in his tone. "My friends and I would never even consider taking over whole countries just because we can!"

"I know," Tower sighed.

Sonic realized they had stopped, and looked up to find the dreaded machine before him. It looked remarkably similar to the trap Eggman had set up for him when he split the world into pieces and awakened Dark Gaia, with some differences. It was protected by a bowl-like structure, with the same machinery open for him to see. In the center of the machine stood a solid metal chair, with cuffs built in where his wrists, ankles, and torso would be. Surrounding the chair like a shield was a cylindrical glass pod, which was open, and the entire thing was closed off by a similar glass wall, which opened up before the group. Sonic shuddered as his memories of the incident with Eggman and the similar machine came unbidden to his mind. If this was anything like that…

Commander Tower noticed his unease and motioned for the soldiers to take him into the machine.

"The procedure won't last long," he said, staying where he was and looking the blue hero in his emerald green eyes. "It will only take about five minutes to complete, but you will feel a significant amount of pain. Let it run its course, and then it will be all over."

Sonic gulped and nodded, seating himself on the chair. The soldiers took off the handcuffs, then secured him to the machine and left, the glass container closing behind them with a hiss. The blue blur gulped again as his claustrophobia kicked in, finding the space and his being restrained much too restricting for his liking. As the final glass wall sealed itself shut, he could barely make out the GUN Commander's grim face, full of regret, as he heard the first hum of machinery start up…

Then he felt the first wave of pain.

...

The streets were crowded by the hundreds of protesters gathered there, still refusing to back down even though it was early morning. The city square, filled to the brim with angry citizens and peace-keeping officers, displayed on their jumbotrons replays of the GUN announcement condemning the four Supers to imprisonment. As the news footage continued to play, suddenly static seeped into the screen, overtaking the previous broadcast and revealing a darkened room. All of the people below hushed and stopped whatever they were doing, seeming to know something significant was about to happen.

At last, a figure stepped out of the darkness. A black hedgehog with red stripes on his arms, legs, and quills walked up to the screen, ruby red eyes staring at whoever was watching.

"People of Mobius," the deep voice rumbled. "You may have heard some disturbing news about a new GUN initiative called Project: Chaos Control. If you are concerned, saddened, or angry, then you have a right to be."

To his right, another hedgehog stepped forth, silvery white in color and normally wonder-filled golden eyes hardened with seriousness.

"Project: Chaos Control is not meant to just capture Mobians with incredible power," he said, his determination hardening his resolve. "It is meant to destroy that power."

Down below, people gasped and shouted curses to the officials as this new revelation unfolded before them.

"As of now, we are considered the highest-level fugitives at GUN," a female voice spoke up as a purple feline with golden amber eyes revealed herself on the first hedgehog's left. "But there is more."

"We have evaded GUN," the black and red hedgehog pressed. "We have found sanctuary. And now, we have your support."

"People of Mobius," the silvery hedgehog spoke again. "We can't continue to protect you without your help!"

...

Sonic cried out as the energy and the pain laced through his body, permeating every part of him. He clenched his teeth to prevent another scream, but choked back a gasp as he felt something shift in his Chaos Energy. Slowly, as though trying to prevent the inevitable, he felt a small part of his Chaos Energy leave his body, replaced by the unbearable pain that completely enveloped him. He thrashed around in his restraints, too overcome with pain and torment to care about preserving his pride. As the tears rolled down his muzzle, he heard a voice he had hoped beyond hope to never hear again.

I've been waiting for you, Controller…

...

"We seek those willing to stand beside us," Shadow pressed to the enraptured crowd. "We ask for your help. GUN may be out to get us, but we refuse to back down from their challenge."

...

It's been so long since we've talked, the voice echoed, a smirk clear in its tone as Sonic screamed at a new wave of pain. It laughed haughtily as the blue hedgehog lowered his head, exhausted.

My, you've gotten weaker since our last encounter, it sneered. I'm afraid I'll have to remedy that.

"N-no," Sonic gasped, horrified as the images of the voice's previous takeovers filled his mind's eye. Eggman cowering in fright, Amy screaming as the roboticizer activated; Tails, mute with shock at the monster his big brother had become. The Metarex, watching with interest as he lost control at the sight of his scared and injured friends. And the latest, struggling to escape Eggman's trap as Neo Metal Sonic closed in for the kill during the final battle…

...

"Do not be afraid because we are being hunted down," Blaze spoke, calm and collected as ever. "Have courage, because we vow to stand beside you, no matter if the world is our friend or our enemy."

...

"No!" Sonic exclaimed, crying as the negative Chaos Energy singed his navy blue fur.

Actually, the correct answer is "yes", the voice laughed. You tried so hard to hold me back, but deep inside you knew one day I would rise again. Well, today's that day. And this time…

Sonic looked up as he sensed a familiar energy signature. His emerald green eyes widened as he discovered the purple and grey Chaos Emeralds securely attached to the machine overhead.

This time I'm here to stay.

...

"We are setting up a network of people willing to support us," Silver said. "No one should be alone in this dark time, and neither should us."

"If you feel you cannot support us directly, then spread the word. Do not let our voice go unheard."

...

"No! You can't-" Sonic choked back a scream, vision blurring. He sensed another shift in Chaos Energy, and recognized the altered energy they had taken from him just before it was shot into the container. The Blue Blur couldn't hold in his screams this time as the altered energy tried to enter his body, tried to neutralize his abilities…

I think I've let you suffer enough, the voice, so much like his own, pondered. It's time to bring me back!

"Y-y-you…" Sonic tried to counter, but the torture was unbearable. The Chaos Emeralds glowed suddenly as negative energy grew in power-and began to alter itself.

...

"We are your heroes. We are your protectors."

...

"Commander, the energy is reversing!" one of the scientists exclaimed from his computer screen. Commander Tower whipped around to speak to him just as another scientist cursed loudly.

"It's rerouting itself into the subject! The level of negative energy is off the charts!"

"The machine can't hold this much energy!" a third yelled.

"Evacuate the base immediately!" Tower commanded. "You six, contain the other subject!"

The soldiers nodded and ran, but as the stairwell doors finally ceased their swinging, Sonic gave one last, tormenting scream. The Commander turned to see what was happening, but everything was engulfed in a brilliant flash of light and a sound of thunder.

...

"We refuse to give in."

...

Mephiles wrung his hands together nervously, at a loss for what to do. Sonic was gone, and his connection to Iblis was cut off. What was he supposed to do now, now that he was little more than a lab rat with an affinity for shadows?

Iblis, what do I do?

The cell door slid open, revealing a squad of soldiers rushing into his cell with cuffs at the ready.

The shade backed away, caught off-guard. "What is the meaning of this?"

One of the soldiers opened his mouth to remind the shade who was in control when a rumbling sound rocked the building, effectively slowing down the soldiers' advance. Just as each person glanced to each other, looking for an explanation, a violent explosion sent everyone and everything flying.

...

The lab was covered in smoke and debris, an occasional fire flickering and casting confusing shadows on the walls. Out of the ruins of what was once a feared mechanical wonder, a lone figure stood to his feet. He blended easily into the shadows, making it hard to discern a trick of the light from flesh and bone. However, if one were to be watching the entire scene, they could never mistake the glow of the figure's pure white eyes.

...

Hands joined together, raised for the crowd to see, as the three Supers made their declaration known.

"We are The Resistance!"

...

Smoke was everywhere, only helping to further annoy the shade as he finally regained consciousness. He groaned and tried to rise, only to get on his hands and knees before the pain in his head forced him to stop. He looked around at the ruins of what was once his cell, finding it satisfying that the soldiers were gone.

How long have I been unconscious? he wondered. A few minutes? Nearly an hour?

He glanced toward the door, surprised but satisfied to find it wide open. He started towards it, but only made it a few steps before his ankle chain grew taut much sooner than before. Mephiles turned, and cursed as he realized a large beam had fallen on the chain, further restricting his movement. He turned around to evaluate it and figure out how to break free, but stopped as he heard a faint voice calling his name.

Mephiles…

Where was it coming from?

Mephiles…

"Who's there?!" The demigod whirled around, forgetting his dilemma as he tried to locate the sound.

"Mephiles…"

The shade turned to the doorway. A large figure stood there, his massive frame almost dwarfing the way to freedom.

Mephiles squinted his reptilian green eyes, trying to make it out, before those green eyes widened with shock.

"Iblis?"

"Yes," the deep voice replied, clearer now. "...And no."

Mephiles screamed as his brother fell at his feet, landing on the cold floor with a dull thump. The shade backed away as far as his tether would allow, a hand clutched to his chest in pure terror.

His brother was covered in blood, something the shade hadn't thought was possible. His green eyes, once full of rage and fire, now stared blindly ahead, nothing more than cold embers.

"It's been so long since I've killed," the voice spoke again, clearly not Iblis as its owner stood in the doorway, taking a few steps into the cell. "I wonder what kind of fight you'll offer to entertain me…"

Mephiles looked up, tears beginning to form. "W-why… why did…" Then, his poison green eyes hardened into obsidian, his shock giving way to rage as he stood.

"Y-you killed him! You killed Brother!" he screamed, fists clenched and ears laid back and flattened against his head. He hated how childlike he sounded, but he couldn't allow himself to dwell on his weakness. His brother's murderer had to be brought to justice, he had to-

His tail involuntarily curled between his legs as his brother's murderer laughed haughtily.

"Yes, I did."

The figure was gone in a flash. Mephiles whipped wildly around, trying to locate his foe. Unfortunately, it was his foe who struck first.

He cried out as a foot kicked him in the back, then gasped as said foot struck him in the stomach. He tried to swing a fist, only to be backhanded and thrown to the ground. The shade scrabbled as far away from his adversary as he could, only to be grabbed by the still active inhibitor collar and lifted up to face the pure-white eyes of his brother's killer.

"My, my, is this any way to greet the great Dark Sonic?"

Part 1 of 3.

*insert fangirl screaming here*

... I have no words. I feel sorry for these characters but at the same time... it's for the good of the plot. And the good of you guys, as well.

Special thanks to my betareader, silvershadowlover on deviantart, for coming up with the idea of bringing Dark Sonic into the mix. I wouldn't have thought of it myself!

Chapter 6 will be posted in about two weeks from today (providing work doesn't get in the way). Till then, have a good day, and kindly leave a review. It really helps!