Woot! I've worked really hard on this, but there probably still mistakes. x.x;; My internet has been out for three days. Three. Whole. Days. Gave me plenty of time to edit and look through, so not much complaint.

Anyways, this is a story that was inspired by a few videos I've seen on youtube and deviant art. The first is by my friend, SonicStorm12, on youtube. The video is called Deception -- ((Dark Sonic)) ~ {What Have You Done} ~ ((Within Temptation)), and it is truely an amazing video. So, go watch, rate, and leave good comments!! That song itself will play a big part in the theme of this story, so keep that in mind. ;)

The other video is an older one. I think it's on youtube now. It's made by mree from deviant art. It's called Sonic: Epilogue. The plot idea is based on both, but more strongly on the second video.

All in all, I think it will be a good one. I'll try to have the next chapter up soon, and maybe I'll update Catcher in the Rye soon as well. ;)

Thanks for reading, and let me know of any mistakes you see!!

What Have You Done?

by Aiko-Chan

Prologue
-game over-

"This is it."

The words broke the silence of the dark room. Eyes slid open to the sound, as if hearing a human voice for the first time. His tiny dungeon was completely black, and he didn't risk movement. He wondered, briefly, if he was still sleeping, if his eyes were still closed. But the desperate feeling in his heart was still there, and he blinked quickly. He needed light to see, room to move.

He tried to move, but the effort was too great. He was exhausted. This was the closest he ever been to admitting defeat.

"You're finally done. I win this time. For good."

A laugh. The voice and strange laughter echoed around him, and he shuddered, as if it hurt him to hear it. He dared to stand, his sore muscles straining against the effort, screaming with stiffness. He blinked again, wondering if he still had his voice. Was it buried somewhere inside him?

Before he could answer the question, lights suddenly blinded him. His hands flew to his face, blocking the brightness from his eyes as they slowly, painfully adjusted. His vision was blurred, but he could see the wall of the small room in front of him. Immediately, he felt better, felt his strength returning, and, with a smirk, found his voice.

"Wow. Didn't think I would make it that time. Pure darkness." A pause, and his smirk widened as he stretched his stiff muscles. "I almost lost all hope."

There was the laughter again, and his smirk wavered slightly. His eyes has finally adjusted, and he could see his dungeon. A small room with an uncomfortable cot in the center, and a large intercom on the ceiling. No windows, no doors, no way out. Fantastic.

"Say what you like," the voice boomed overhead. "But, in a few moments, you'll see exactly what I mean." Another laugh, and the room grew completely silent.

His green eyes blinked, ears ringing. He sighed, sitting back down on the cot and pulling his knees to his chest.

He had been captured six days ago. The longest he had ever been captive. And, so far, this is all that had happened. For six days, he had been stuck in this room. In darkness. This - the voice taunting him from the intercom - was the most interesting thing that had happened so far.

He yawned, wondering where his friends were. They were all probably looking for him. They'd never find him here. The building where he was held was hidden deep within the forests of the Mystic Ruins. He sighed again, eyes narrowing. He wished he knew what the man was up to already. He looked up at the intercom and flashed an obscene gesture before lying down on the cot, arms tucked behind his head.

There was a sudden rumbling all around him. He leaped to his feet, startled. Like an elevator, his room jerked upward, nearly sending him to the floor. The room finally came to a sudden stop, nearly knocking him off his feet once more. Now, he was in what looked like a huge glass container, and he walked forward, placing his hands on the glass and looking outside.

He was in a wide room, filled with robots and machines. The metal floor was a dark red, reminding Sonic of blood. The walls were painted silver. A monitor beeped on the opposite wall, several pictures of the outside world flashing on the many screens, and he wondered where all the cameras could possibly be hidden. Already, he was coming up with an escape plan; the closest exit was near the monitors, and with one spindash, all of the robots that were coming to life could be destroyed. He grinned again.

"Welcome, hedgehog!" the booming voice said, only this time, not as loud. He looked up to see the wide scientist floating down from the ceiling on a hover disc. Humorously, he wondered how the thing stayed above ground. He crossed his arms.

"Hello there, Eggman!" he retorted, throwing up his hand and looking around the glass dome he was stuck in. "So, uh, when do you plan on letting me out so I can kick your ass?" He tapped his finger against the glass lightly, his green eyes alight. Dr. Ivo Robotnik laughed louder, and Sonic the Hedgehog's grin wavered once more. Not the response he was looking for.

"Sorry, hedgehog, but that's not what's happening today." He clapped, and for a moment, Sonic was confused. Clapping? Was it a new toy of his? His question was answered with a loud beep, and when Sonic turned around, he watched as gas began to fill the glass dome he was in. Struggling not to panic, Sonic retreated to the corner of his prison, taking a deep breath of what little non contaminated air there was. After a minute, he became lightheaded, and nearly collapsed. He was forced to give in just as his vision was becoming black. The gas filled his lungs, burning his throat and eyes, and he felt every muscle in his body fall limp, and he collapsed. He couldn't move.

As he struggled to move his frozen limbs, the gas began to disappear, and the glass dome lifted. A large robot clanged over and scooped him mercilessly in his metal arms, carrying the paralyzed hedgehog to a nearby table outside his prison. He felt his mind switch into panic mode, and he struggled harder. Still, not a muscle moved.

He was thrown down on the table, and he grunted on impact, feeling the robot twist his arms behind his back. Within moments, he was tied up. The hedgehog had never felt so helpless. When released, he fell on his side with a grunt, his face smashed against the table. He watched, slightly fearful, as Eggman approached, a smug grin on his fat face.

"Comfortable?" he laughed, walking closer. Sonic felt sick, and didn't reply. "I told you, hedgehog, I've won this time. It's over." His grin widened as he closed in on Sonic, face inches from his. The hedgehog cringed at the smell of his breath, and still, even in his troubled state, replied with a usual witty response.

"Ever heard of a toothbrush, Eggman? Shesh!" Sonic faked a cough, and the scientist's grin twitched slightly. His eyes flashed, and his hand shot out, grabbing Sonic around the neck none-too-gently. The hedgehog gasped, one eye closed as Eggman squeezed his windpipe.

"You'll regret everything you've ever done to me, hedgehog," he whispered, scathingly, hatred clear in his voice, and Sonic felt a cold chill travel up his spine. All of his life, he had believed it was a game. Cat and mouse. But the evil, cold look in the scientist eyes said otherwise. "I'll take from you as much as you've taken from me, and more." Just as Sonic was becoming lightheaded, Robotnik released him, and he grunted as his head struck the table hard, wincing. He watched as the evil scientist walked toward the monitor, pushing a single button. Sonic watched helplessly as four large poles popped up around him. His breathing hitched, fear finally seeping into his veins.

"I'll enjoy watching this hedgehog," came the scientist's cold voice, and he laughed before jerking a switch on the monitor. Eyes widened, Sonic heard a crackle just milliseconds before pain gripped him. He cried out, feeling the electricity course through his bod, jerking and flopping involuntarily. Over his cries of pain, he heard the scientist cackle madly, and all Sonic could think was how heartless the bastard truly was.

Sonic watched the world spin and shake, watched his vision fade from red to black and back again. For awhile, he wondered if this was it. If Eggman simply wanted him dead. The pain was so intense, Sonic hoped it would come sooner rather than later.

What seemed like hours later, the pain was gone, and Sonic gasped and panted for breath, every bone and muscle in his body feeling raw and bloody, tense. With one eye opened, he watched as Eggman got closer, something clutched in his meaty fingers.

"This...this will make you regret everything," the scientist cackled madly, his hand raising above the hedgehog's motionless body.

It didn't take long for Sonic to realize it was a syringe filled with a green liquid. He neared Sonic with the needle in his hand, his eyes glinting strangely behind his glasses.

It was then that Sonic knew it had never been a game. The scientist was twisted, demented, and with every loss suffered at Sonic's hands, he became more and more determined to achieve his goal. For the first time in his life, the hedgehog was feeling the icy cold fingers of fear touch him. Never before had he feared for his life. But watching the crazed scientist near him with the mysterious needle, the feeling was strong in his heart. But what could he do? The hedgehog didn't have the strength to fight or try to move. He simply lie there, watching as the needle came closer to him.

"With this, I won't have to lift a finger. You will do all of the revenge for me." This got a reaction. Sonic's green eyes narrowed and widened, and he finally found the strength to struggle. He had an idea of what would happen if he was injected with that stuff. No! He couldn't hurt them!

But what could he do? It was over. And with a sickening, dropping feeling, Sonic knew it was true. There was no escape. He had lost this time. This final time, when it mattered most, Sonic lost.

"Goodbye, Sonic. At last, I've won!"

He stabbed the needle into the hedgehog shoulder, injecting all of the liquid at once.

A deep bloodcurdling cry sounded from Sonic's lips as the needle pierced his skin. He felt the liquid spread like fire through his veins, burning him, scalding hot. Liquid fire. His vision flickered, his mind racing.

It's can't end like this! he screamed in his mind. But he knew it was too late.

As the drug made its way to his heart and his brain, Sonic could only think of his friends. His eyes closed as he saw all of it. His home on the cliff in the Mystic Ruins. Knuckles, the Master Emerald and Angel Island. Amy and that stupid hammer she always carried around. And Tails. He saw Tails fighting with him, playing with him when he was a child.

How, even being controlled by evil, could he hurt them?

Tears dripped down his face, from pain and grief. They flashed red, then back to green. His head felt like it was going to explode. He was shaking violently, the fire flowing through his veins burning, burning, burning.

And, suddenly, with a fiery explosion, the wall with the monitors exploded, and as the rubble fell away, a young orange kitsune leaped through the flames. Tails.

"No!" Sonic screamed, his eyes flashing wildly. Green. Red. Green. "No! Tails! Leave! GET OUT OF HERE!" The kitsune's blue eyes flashed to him, shock etched in his face. Sonic screamed again. "GO!" The last thing the hedgehog saw was his younger brother's shocked, terrified face.

I'm sorry, Tails.

Green eyes flashed red a final time, blue fur was replaced with black.

Tell them I'm sorry.

A final scream, and Sonic was gone.

He knew it was a risk, but Tails demanded that he enter the lair alone. Knuckles and Shadow were to wait outside, keeping guard.

As Tails sleuthed through the hallways of the lair, he worried, briefly, about Sonic. The hedgehog had been gone for nearly a week after his capture. Sonic had told Tails before their raid on Robotnik's airship that, if he were captured, to not come after him. That he would escape. Of course, Tails had no intention of listening.

During their raid, something had went wrong. As they had swiftly fought through the walls of robots, a security device had went off, to both their surprise. In a final act of desperation, just as they were overwhelmed by robots, Sonic had grabbed Tails and, without a word, shoved him from the airship. The kitsune, shocked, quickly took flight, and watched Sonic disappear under an army of robots.

"Go!" he had cried during his struggling. "Find Knuckles and Shadow! I'll be fine!" Tails reluctantly obliged, and immediately went to find his two companions.

Six days later, here they were.

Tails ran through the hallways, dodging attacks from robots patrolling. It took him longer than he would have liked, but he finally found the control room. Using a miniature wall bomb, the kitsune had blown the wall up, flying into the control room bravely.

"No!" Sonic screamed, his eyes flashing wildly. The kitsune's blue eyes found him, violently jerking on the opposite side of the room. To say the kitsune was shocked was an understatement. "No! Tails! Leave! GET OUT OF HERE!" He was too shocked to move, but knew he wouldn't leave regardless. He could see the flashing of Sonic's eyes, hear the desperation and fear in his voice. "GO!" This last cry finally got his attention, and the kitsune leaped into action.

"Sonic!" he screamed, leaping toward the bond hedgehog. "Sonic, hang on!" But, he knew he was too late. The hedgehog fell limp, his violent struggling stopping suddenly, abruptly. Nearby, Tails heard the insane laughter of Robotnik, crazed and demented. Still, Tails ran, refusing the believe what had just happened. He stopped at the hedgehog's side, eyes wide and his heart heavy. Was he breathing? The kitsune reached out with one hand, slowly, carefully, just barely grazing the motionless hedgehog's shoulder. A single tear dropped from the hedgehog cheek, dropping to the floor, and Tails' breath hitched in his throat.

"Sonic..." he breathed, his eyes filling with tears. Was it true? Was he gone?

No...No, he was still breathing!

"Sonic!" he said a bit louder. "Sonic, are you okay? Please be okay..."

He touched his shoulder gently, a gentle grip. And, suddenly, his eyes flashed open. But they weren't the friendly green Tails was used to.

They were a lifeless red.

Tails couldn't move. Couldn't speak. All he did was remove his hand from the hedgehog should, gaping at the red eyes and dark fur. A blink, and the red eyed, dark furred hedgehog grinned coldly.

"Sonic?" he said in an icy voice. A chuckle. "Sonic's not here anymore."

Tails took a single, terrified step backwards, and the hedgehog shot forward. With a strangled cry, the kitsune swiftly leaped out of the way, watching as the hedgehog leaped into the air, curling into a ball and spinning. He whipped back around like a boomerang, spindashing right through several of Robotnik's machine and robots. Flames erupting around them, and Tails felt the heat nearly burning his skin as he turned away from the flames, a cry in his throat.

"What?!" Tails heard the disbelieving cry of the scientist as half of his inventions were destroyed. But Sonic wasn't finished yet. He continued spinning through the air, doubling back toward more of the scientists machines. Explosion after explosion. And yet, Tails couldn't move.

An evil cackle came from above him...and it wasn't Robotnik's. A black blur broke through the roof of the building, sending debris falling around Tails. Breaking from his trance, Tails knew he had to leave. An orange blur against the flames, Tails flew up to the hole in the ceiling, watching as the dark-haired Sonic flew past him midair. For a moment, time seemed to stop as red eyes met blue, and Tails knew;

Sonic was gone.

Tails flew out of the building, landing nearby moments before Robotnik came flying - quiet literally - out, thrown from the building by Sonic. The evil hedgehog emerged seconds later, a smug smirk on his face.

"That...that wasn't supposed to happen," came the quiet, horrified voice of Robotnik. Tails was frozen again, his blue eyes wide with horror and disbelief, glued on the dark version of his best friend, his older brother. He couldn't breath

For a moment, Sonic turned to him, and Tails wondered if Sonic was buried there somewhere. Bravely, he uncovered his voice, taking a single step forward.

"S-Sonic," he breathed quietly, almost a whisper. Tears filled his eyes again. "Sonic...please...it's me..." Red eyes met blue again, but the smirk didn't disappear. There was no friendliness in that stare, no recognition. Instead, the hedgehog's eyes darted back suddenly to the frozen lump of Robotnik huddle against the ground. The hedgehog moved swiftly, lunging torward the motionless scientist. The kitsune watched as Sonic attacked, and, with one blow, sent Robotnik back to the ground, dead where he fell.

Horrified, Tails simply stared. Robotnik layed in a crumpled heap at Sonic's feet, the hedgehog's arm still raised from the attack. His heart was pounding in his ribs, hard, and he wondered briefly if the dark hedgehog could hear it. He couldn't tear his eyes from the motionless form of Robotnik. Then, the dark furred hedgehog turned to him, his red eyes glaring. The smirk was gone, replaced by a frown. Tails finally tore his eyes away from the dead scientist to the red eyes of his best friend.

For a few moments, it was a stare down. Neither moved. Tails felt the adrenaline pour through his veins, terrified and deeply scarred. He knew that if it came to a battle, he couldn't harm Sonic. He didn't have the emotional strength to harm his best friend, whether it was simply his shell or not. Tails didn't let this show, however, and simply stared back, fighting against the tears that plagued him.

"...Sonic..." he whispered, eyes watering. "Sonic....why?" There was silence after he spoke, and still no movement. Then, the dark hedgehog grinned again.

"How many times do I have to tell you, rat?" the hedgehog spoke. Sonic's voice, Sonic's grin, Sonic's body...but not Sonic... He braced himself to leap, and Tails held his breath. "Sonic's gone. That weakling will never come back."

"Tails!"

It was only then that Tails remember Shadow and Knuckles hidden somewhere nearby. The bushes rustled, and the dark hedgehog jerked, surprised. His grin wavered a moment, but his eyes darted back to Tails, glinting in evil amusement. Tails still hadn't torn his away.

"See ya later, rat," the hedgehog laughed. "It'll be you and your friends' turn soon enough!" Tails watched as the hedgehog took off, disappearing into the woods. He could still hear his footsteps, even after Shadow and Knuckles appeared from the bushes, wild eyed and shocked.

"Oh, my God!" he heard Knuckles shout loudly. "What the hell happened?" When Knuckles approached the still body of Robotnik, Tails only then realized he was still holding his breath. He gasped for air, tears finally leaking from his eyes as his eyes focused on Robotnik's body. Shadow was silent, simply looking toward the forest, right where Sonic had disappeared moments before their arrival.

"Tails!" he heard Knuckles shout several times before a swift slap to the face jerked him from his trance. The kitsune's eyes flew wildly to Knuckles, and he gasped again. "Tails! What happened?!" The kitsune's tails spun wildly behind him.

"Sonic!" he sputtered. "No...not Sonic... He's gone, Knuckles! He's gone! He killed Eggman! He killed him! Right there! He...he almost...almost..." He almost killed me! He couldn't finish the sentence aloud, and the kitsune shut his eyes tight, hoping maybe all of this was simply a bad dream. But he felt his hammering heart, his pounding head, his broken heart, and knew it wasn't so.

Knuckles was silent, and when Tails opened his eyes again, he saw the echidna huddled over the scientist body, his violet eyes wide and disbelieving.

"...Sonic did this?" the echidna whispered. "He couldn't. That hedgehog doesn't have a murderous bone in his body.... He couldn't have... He just couldn't have..." Knuckles rounded on Tails suddenly, and the kitsune stepped back, startled. "Are you positive?! What happened when you got in there?! What did Eggman do?!"

"He...Sonic was just...just shaking...so hard..." The words came between quiet sobs. "He...he yelled at me a-and told me...to leave...to get out..." He paused, his voice breaking at the end, and he dropped his head into his hands, feeling too weak to stand. "Then he...h-he just...collapsed... When his eyes opened...t-they were red...blood red... And he kept saying he...w-wasn't Sonic..." A sob. "He's gone, Knuckles! He's gone!"

There was silence again.

It was Shadow who spoke next, and Tails almost forgot about his presence. "Apparently, Robotnik had suffered enough losses." He spoke calmly, darkly, and Tails could almost curse him for being so calm. "So he came up with a chemical to turn the hedgehog evil." Shadow approached the dead scientist, kneeling next to him. "Seems it worked...backfired a bit on his part."

Tails and Knuckles were silent. Tails stared at the body through blurred vision, having no idea what to do next. Shadow finally stood, and Tails watched him, blue eyes shining with tears, his mind foggy, and his heart heavy. The dark hedgehog turned and face the echinda and kistune, blinking slowly.

"If I had to bet," he spoke again, stepping closer to them and looking toward the ocean. "Our new friend will be killing everything and everyone in sight..." His dark eyes blinked, and he paused for a heartbeat. "...unless someone stops him." His dark eyes landed on Tails and Knuckles, each for a heartbeat.

"What...you mean, kill him?" Tails responded, and Shadow looked at him without a response. The kitsune's blue eyes narrowed. "There's...there's got to be another way."

Shadow blinked, unperturbed.

"If you can think of one, be my guest."