Flying over Station Square, a black helicopter was heading to an undisclosed location. The pilot was on the radio, speaking with dispatch.
"This is Sigma-Alpha 2 heading due south over the city. We're enroute to base."
"Copy Sigma," dispatch replied. "Be advised, cargo is considered volatile and dangerous."
In the main part of the plane, Sonic was sitting there surrounded by soldiers. His hands were cuffed and the soldiers looks were a mixture of confusion and worry.
"Everything ok, boys?" Sonic asked.
One of the soldiers looked over, struggling to speak. Finally, he managed to get his words out.
"Did you do it?"
"Depends. What do you think I did?"
"You attacked Prison Island," another spoke up. "You broke in and trashed the joint."
"Is that so? Well it's the first I've heard about it."
"Gyah, I knew there was something fishy going on," a third soldier let out. "Sonic would never do anything like that."
"Pipe down!" the pilot shouted. "We'll be arriving at G.U.N. in 30 minutes, then they can deal with this freak."
Sonic just gave a knowing smirk.
…
Mere seconds later, Sonic forced the door of the copter open. One of his cuffs was off, the metal restraints dangling from one wrist as he looked out at the city below.
"Talk about low budget flights!" Sonic remarked, leaping out onto the outside of the copter. "No food or movies? I'm out of here. I like running better!"
Sonic then tore off a metal plank and leapt off the copter with it. Riding it as a snowboard as he spun midair.
…
Once Sonic reached the ground, he rode his metal board down the street as fast as gravity would carry him. He swayed from side to side, brushing his hand against the street as he rode along. He jumped over a few parked cars, and even grabbed onto a lamp post to make sharp turns. While riding along, he soon became clear of some flying robots that were pursuing him.
"Definitely not Eggman's," Sonic noted. "Wonder who made them."
Veering right, Sonic leapt off an interpass and quickly kicked his board into a pursing robot, destroying it. Once on the ground, Sonic made a break for it, dodging the constant laser fire from the robots. Thinking fast, Sonic saw a nearby manhole cover and kicked it up, grabbing it and spinning it around so he could lob it at the pursuing robots, destroying them instantly. Sonic let out a breath of relief before hearing a loud honking sound. Sonic looked behind him and saw a massive truck barreling towards him.
"Uh oh!" he let out. "That's not good!"
Sonic instantly took off in the other direction, with the truck hot on his trail. Sonic rounded the corner to try and evade the truck, but it maintained pursuit, slamming into the side of a building as it did so.
"These guys don't care who gets hurt as long as they catch me," Sonic realized. "Just who is the G.U.N, and why are they after me?"
…
Meanwhile, the President was having a meeting with Christina about pressing issues at hand.
"Our undercover agent has integrated himself well," Christina reported. "And is in a primed position to gather the necessary information on the ARK incident."
"Excellent. And the flood?"
"Well, sir, I've read the full report over the last few days. There was some damage, and more than a few casualties. However, we were fortunate to have Sonic arrive when he did. Without his help, I'm almost certain Station Square would still be underwater."
"Speaking of which, are we sure about Sonic's involvement in the Prison Island incident? I know Sonic and this seems wildly out of character."
"I agree sir, however, G.U.N. has provided security footage of Sonic breaking into Prison Island. They have yet to disclose exactly what he did while he was there, but they insisted that he must be captured immediately."
"And what do you suggest?"
"Honestly sir, I'm not sure. There's clearly something going on, but we're lacking vital information."
"Then I'm afraid we'll just have to wait until we know more."
From the driver's seat, Sam's hands tightened on the front wheel.
"Sir, permission to make a phone call?"
"I suppose so," The President allowed.
…
Back with Sonic, he continued running from the pursuing truck, looking for any way to take it out of commission. Passing by a nearby construction site, he quickly got an idea. He sped inside, snagging some spare nails that were laying about, and sprinkled them in front of the truck's path.
"Hey big guy! Right here!"
The truck roared towards Sonic, the wheels running over the nails and exploding. The truck skidded across the road, rolling onto its side before finally toppling over. Sonic smirked before running off, hoping to put some much needed distance between him and whoever was chasing him.
"Who are these guys? And why do they think I'm some kind of criminal?"
…
At the Kent house, Keith's phone began ringing. Keith was quick to answer it once he saw it was Sam.
"Hey Sam, what's up?"
"Hey bro, have you heard from Sonic lately?"
"No, not since a few days ago. Why, something happened?"
"You might say that. Look, you didn't hear this from me, but Sonic is in a boatload of trouble. Some government flunkies called G.U.N. are trying to arrest Sonic for god-knows-what. You need to find him and get him to safety before something happens to him. This is big Keith. Big enough that even the President is in the dark."
"Whoa… thanks for the heads up. I'll try and find Sonic fast."
He hung up, instantly worried. He then flipped through his contacts, dialling Kat. After a few rings, it connected, but there was some serious wind in the speaker.
"Oh shoot! It happened again!" Kat cried out before there was a loud thud and the wind died out. "Hey Keith. Sorry. You caught me in a wind funnel. What can I do for you?"
"I was hoping to get your help on something. Sonic might be in trouble."
"Wish I could, but me and Knuckles are kinda in the middle of- HEY! Knuckles! Rouge stole my bag!"
Keith heard what sounded like cursing then the sound of a fight in the distance.
"Drop the satchel, batgirl!"
"Not a chance, Knucklehead! These pieces are mine!"
"Hey, hey! Watch the bag! You'll tear the leather!"
"Uh…. Kat?"
"Sorry, sorry. Look, long story short, the Master Emerald got shattered again and we're on another scavenger hunt. Unfortunately, a certain BAT WON'T LEAVE US ALONE!"
"Just give me what I want and I'll leave!"
"I see… well, clearly, you've got your own problems to sort out. I'll leave you to it then."
"Thanks dude. Good luck with-"
There was another thud and the call cut out. Keith looked at the phone for a moment, then put it back in his pocket.
"Man. Just when you thought everything could go back to normal."
…
That night at a museum, a green Chaos Emerald was on display in one of the wings. As it just sat there, the silhouetted form of a hedgehog slowly approached the display. He shattered the glass surrounding the Emerald, causing alarms to sound as he snatched it and took off. Once he got outside, he was immediately surrounded by several G.U.N. Beetle robots, hovering over him. The hedgehog just smirked as the Beetles opened fire, prompting him to leap around the blasts before jumping up and smashing one robot after another, instantly wrecking them. Once the Beetles were down, the hedgehog disappeared into the night, leaving destruction and deception in his wake.
…
At a small diner in the city, the patrons were going about their meals as a news report played on the TV. One of the patrons was a Mobian, one wearing a vest over a hoodie, the hood covering their head as they just ate their food. Suddenly, the TV switched to a new story.
"We interrupt this broadcast with an important newsflash. There has been a break-in at the Station Square Museum of Natural History today. Mysteriously, the only thing that was stolen was a Chaos Emerald. According to officials, the suspect has been identified as the world-renowned hero, Sonic the Hedgehog. The suspect was seen fleeing the scene, destroying the museum's guard robots in his path. Stay tuned for more details."
Everyone in the diner began talking among themselves as the Mobian lifted their head, looking at the screen. It showed Sonic smashing through the Beetles with no remorse. The Mobian stood up, lowering their hood and revealing themselves to be none other than Chessie.
"Sonic?"
…
Back at the Kent house, Keith went to find Tails, who was working with Chuck in his lab. As he came rushing into the room, he found the pair staring at the TV, watching the same broadcast that had been playing in the diner.
"You know too?" Keith asked.
"We do," Chuck replied. "And we can't believe it."
"There's no way Sonic could've done any of these things," Tails insisted. "No way!"
"Sam thinks something's going on," Keith explained. "Even the President is in the dark."
"Well whatever's going on, we need to find Sonic!" Tails insisted.
"Agreed," Keith replied. "But I don't have a clue on where to look."
"Well we'd better start looking soon," Tails insisted. "Otherwise, someone else may find him first."
…
Down in the sewers, Sonic walked along the dark tunnel, finally glad to catch a break from the robots chasing him. As he walked along, he saw a fire glowing not too far away, realizing that there were some homeless people up ahead. They seemed to be talking amongst themselves as they warmed themselves by the fire.
"I'm tellin' ya, everyone's after him. They say he robbed the museum."
"Git out. Ain't no way he would. He ain't that kinda guy."
"Nice of you to think so," Sonic voiced, causing all of them to turn towards him.
"It's him!" One of the homeless called out. "What're you doin' down 'ere, Sonic?"
"Catching my breath. Mind if I join ya?"
They all scoot, making room for Sonic by the fire. He sits down.
"What's going on up there?" One of the homeless asked. "Everyone's sayin' yer actin' outta character.'
"It isn't me, I can assure you. Someone's trying to ruin my good name."
"Think it's that Robotnik guy?" another man asked. "He seems like the type."
"Maybe. It's not the first time he cooked up a double of me, but I trashed it months ago."
Just then, a low rumbling started echoing through the tunnel. Sonic looked down the tunnel and saw several G.U.N. Beetles rushing towards him.
"Uh-oh. Gotta go!"
Sonic instantly took off down the tunnel, leaving the homeless behind as he beat feet back to the surface.
…
At the White House, Agent Stone appeared before the President to inform him of the situation.
"Mr. President, there's been a new development," He announced. "I'm sure you've heard about Sonic breaking into the museum and stealing the Chaos Emerald."
"I have," The President replied. "Are you certain it's him?"
"Positive. My units are pursuing him now. We'll have him cornered shortly."
"Very well. However, I want him brought in alive. I want to hear what Sonic has to say before this situation gets out of hand and we do something we'll regret."
"Of… course, sir," Agent Stone replied after a moment.
Agent Stone then exited the Oval Office, pulling out a communicator.
"This is Agent Stone, the President has given the go ahead. Maintain pursuit on Sonic… and shoot on sight."
...
Meanwhile on Prison Island, Scarlet and Franklin were driving up to the main gate. Scarlet looked around in absolute awe.
"How on Earth did you manage to get permission for us to be here?" she asked.
"Let's just say I'm well connected," Franklin replied.
He reached into his pocket, pulling out his government ID and flashing it at the camera. After security verified its authenticity, the doors opened and they were allowed inside. He tucked it back into his coat, but not before Scarlet got a good look at it.
"Just who are you?"
"Just a fellow news hound, that's all."
The two drove inside.
...
Once inside, the two were greeted by the warden of the entire facility. They met in his office, beginning their interview.
"Sir, what can you tell us about the ARK incident?" Scarlet asked.
"I'm afraid I can't give you many details. That was long before my time."
"Well then, what can you tell us about the break in last night?" Franklin questioned.
"You know the official story," the warden replied, playing footage on a monitor behind him. "Dr. Robotnik and the hedgehog broke into the system and tried to steal military secrets."
The pair watched the footage as Sonic aided Dr. Robotnik in destroying several of the robots. Scarlet gasped in shock, but Franklin's eyes narrowed, something about the footage feeling off about him. The warden didn't seem to share their sentiments as he ended the footage.
"This video confirms that Sonic the Hedgehog no longer has any concern with the safety of our citizens."
"Can you really be certain about that?" Franklin challenged.
"The evidence is right here. What more do you need?"
"Well, what happens to Sonic now?" Scarlet questioned.
"Quite simple. We find him and arrest him for high treason."
…
Back with Sonic, he blasted his way out of the sewers, leaving a trail of destroyed robots in his path.
"Man, this is getting monotonous." Sonic commented. "I'm out of here!"
Before Sonic could run, a spotlight turned on, blinding him for a moment. As he blinked spots from his vision, one of the G.U.N. bots dropped down in front of him.
"Spider Troop Bigfoot reporting to headquarters! Hostile has been located!"
"Copy that, Bigfoot. Orders are kill on sight."
"Understood."
"Somebody wants to play," Sonic noted. "Ok, bring it on!"
Bigfoot immediately opened fire on Sonic, prompting him to move out of the way. Sonic then leapt at Bigfoot, spindashing between its top panels and taking out its search light.
"Talk about a tight squeeze," Sonic remarked, landing behind him.
Bigfoot just turned around and opened its top panels, revealing missiles that fired right at Sonic.
With a yelp, Sonic raced up a building with the missiles hot on his heels. Once he reached the top, he pushed off, heading right for the robot. He landed on top of it, punching through the glass and grabbing the pilot.
"This is one fireworks show you don't want a frontrow seat to."
He pulled the pilot out, jumping clear as the missiles utterly destroyed Bigfoot. Sonic dropped the pilot on the ground, knocked unconscious by the explosion, then gave a stretch.
"Just sleep it off pal," he told him.
Just then, Sonic could hear something behind him, prompting him to roll his eyes.
"Another bozo wanting a shot at me? Well I'm ready no matter-" Sonic's words died in his mouth as he turned around. "What?!"
The sight Sonic saw left him completely speechless. Standing on top of Bigfoot was a black hedgehog with red highlights in his spines, a patch of white fur on his chest, and golden rings on his wrists and ankles.
"So, you're the famous Sonic the Hedgehog," the newcomer remarked. "I must admit, there is something of a resemblance. If just barely.
"You…" Sonic let out before getting serious. "Now I get what's going on. The military has mistaken me for the likes of you!"
"Yes… and no. You see, your government doesn't want to admit I exist, or the crimes they commited. They've decided to use you to cover up my existence."
"Leaving you free to do whatever. So, what are you up to?"
"Now that would be telling. Just know it starts with this," the hedgehog held up the green Chaos Emerald. "A jewel containing the ultimate power."
"That's the… Chaos Emerald! What are you going to do with that?"
The hedgehog stayed silent.
"Say something, you fake hedgehog!" Sonic let out, running right at him.
The black hedgehog just smirked, holding the Emerald overhead.
"Chaos Control!"
The Emerald suddenly started glowing, engulfing Shadow in a light that caused him to disappear. As Sonic ran, he thought he could see Shadow streak past him, causing him to skid to a stop.
"No way! He can cause Chaos Control with just one Emerald?! Who is this guy?!"
"My name is Shadow," the hedgehog answered, standing on a nearby rooftop. "I'm the world's ultimate lifeform."
"Ultimate nothing!" Sonic threw back. "You're just a two bit faker to me!"
Sonic quickly ran up the side of the building to reach him, only for Shadow to disappear again.
"Not again."
"Faker?" Shadow asked from another rooftop across the street. "I think you're the fake hedgehog around here. You're comparing yourself to me? Ha! You're not even good enough to be my fake."
"I'll make you eat those words!"
Sonic ran back down to the street, with Shadow following after, skating on what appeared to be rocket shoes.
"You won't even get the chance!" Shadow promised.
…
Back at the Kent house, , Chuck was on the phone, looking worried.
"You're kidding! Unbelievable. Well, be sure to call us right away if anything else happens." He hung up, turning to Keith and Tails. "That was Dr. Birnbaum. Apparently Sonic's been spotted battling a government robot on Downhill street."
"Then that's where we're going!" Keith declared. "Come on, Tails!"
"Right!" Tails nodded.
The two bolted out of the lab, Chuck watching them in concern.
…
Meanwhile, Sonic and Shadow were racing down the street, Shadow cutting in front of Sonic.
"Pathetic," Shadow jeered. "You think you can beat me?"
"Don't count me out yet!" Sonic remarked.
He tried swinging a leg at Shadow's head, but Shadow easily ducked under it, delivering a series of punches to Sonic's stomach. Shadow then uppercutted Sonic, knocking him into a lamp post.
As the fight continued, Keith drove himself and Tails down to where Sonic was spotted. The two racing hedgehogs started approaching the car and Shadow vanished. Keith hit the brakes and Sonic skidded to a stop.
"Sonic, what's going on?!" Tails called out.
"I wish I knew, pal!"
Suddenly Shadow appeared behind him, kicking him in the back of the head. Sonic skidded across the ground as Shadow stood over him.
"You don't honestly think you stand a chance, do you?" Shadow boasted. "I've only given you a fraction of my true strength."
"Leave him alone!" Keith shouted.
Shadow turned, leaning to the side to avoid an energy ball aimed at his head.
"Impressive toy kid," Shadow commended. "But still nothing compared to me!"
"Leave them alone, Shadow," Sonic insisted, getting back to his feet. "Fight me!"
"Very well. I have no desire to battle children anyway."
"I'm 16! Why does everyone keep calling me a child?!"
Shadow turned back to Sonic, who was still a little weary from the battle. Just then, the sound of sirens filled the air.
"It seems you have greater concerns to worry about," Shadow noted. "Farewell. Chaos Control!"
With that, Shadow warped again, disappearing as the authorities arrived. Several beetles surrounded Sonic as soldiers got out, aiming their weapons at the weary hedgehog.
"Sonic the Hedgehog, you are under arrest! Any attempt to resist will result in lethal force!"
"No way!" Sonic insisted. "I'm not the guy you want! You gotta believe me!"
"Surrender now, or die where you stand!"
"Sonic, just stand down!" Keith warned. "They'll kill you if you dont!"
"They won't be able to hit me!" Sonic challenged.
"Last chance, Sonic!" the agent replied as another off to the side readied his shot. "It's either a cell on Prison Island, or a bullet. Your call."
Sonic suddenly perked up.
"Wait, did you say Prison Island? That's where you're taking me?"
"Make your choice Sonic! You have to the count of five!"
Sonic stopped for a moment, pondering the situation.
"One… two… three... fo-"
"Ok, I'll give," Sonic replied.
The G.U.N. commander was caught off guard.
"What?"
Sonic got on his knees, putting his hands behind his head.
"I surrender. Just go easy on the wrists, okay?"
"Sonic?" Tails let out.
"It's gonna be ok, pal," Sonic reassured. "But I'll need your help to find the truth. Can I count on you?"
Tails instantly had a look of determination.
"Always."
Sonic shot him a smirk as an officer came over to cuff him. His hands were put behind him this time, causing Sonic to wince as his arms dug into his spines, then he was pulled to his feet and ushered towards a helicopter, the very same one he'd escaped from earlier..
"No more funny business, freak," the pilot snapped.
"Not this time," Sonic reassured.
He was shoved into his seat, these soldiers nowhere near as understanding or compassionate as before. It made Sonic feel more than a little uneasy as the helicopter closed up and took off. Keith and Tails watched it take off, Tails' tails twitching nervously. Keith was gritting his teeth, turning off his gloves before grunting and kicking a stone.
"He's innocent..." he growled. "We have to get him out. I don't know how, but we have to."
Off in the distance as the helicopter took off, Shadow watched with determination of his own.
"Hope you enjoy your stay Sonic. I won't let you or anyone else stand in my way…" He closed his eyes, his fists clenching. "Maria…"
…
At Robotnik's secret base, Orbot, Cubot, and Bokkun were all celebrating Sonic's capture.
"Yippee!" Cubot declared. "We did it!"
"We actually did it!" Orbot agreed. "I never thought I'd see the day!"
"I can't believe the government actually thinks Sonic and Shadow are one and the same!"
Bokkun remarked. "They look nothing alike!"
"Willful ignorance perhaps?" Orbot suggested.
"Who cares?!" Robotnik shouted. "Sonic's been locked up for good thanks to our new pal, Shadow. I will admit, I was quite skeptical when he first woke up..."
…
Robotnik placed the Chaos Emerald in, powering up the machinery. Steam hissed from the pipes as the machinery powered on. The ice began melting away from the tube before finally opening up. Robotnik stepped back in shock as the creature rose, turning towards him.
"It… can't be…!" Robotnik let out, seeing the form of a hedgehog. "Is that you Sonic?! I've come too far to let you-"
Suddenly the smoke cleared, revealing someone else all together.
"Wait a minute, you're not Sonic. Who are you?"
"My name is Shadow," the creature informed, leaping out of the capsule. "And since you were so kind as to release me, my master, I will grant you one wish."
Just then, an alarm started blaring, causing Robotnik to growl.
"Now what?!"
A new robot entered the room, closing in on the invaders and the freed hedgehog.
"This is Scorpion troop Hotshot, enemies have been detected. Enroute to destroy!"
"Hold," Shadow told him. "And witness the true power I possess."
Shadow then darted at Hotshot, zipping around its blaster fire before leaping up to him. Shadow then smashed the robot's turret before summoning some energy from his hand and blasting its leg. The robot staggered to keep balance as Shadow landed on the ground and leapt up to the cockpit, destroying it and causing the robot to topple over before exploding.
"That was spectacular!" Robotnik let out. "Alright Shadow, I'm convinced. You really are my grandfather's ultimate weapon. But what did you mean when you said you would grant me a wish?"
"All in good time." Shadow started walking off. "First we need more Chaos Emeralds."
"Wait, where are you going?!"
"I'll be waiting for you. In the central control room on the Space Colony ARK."
"ARK?!"
…
"Speaking of which, it's high time I had that meeting. Is the space transporter ready?"
"Indeed Doctor," Orbot confirmed. "Coordinates are set to the ARK. Though why he would want to meet in a dingy place like that is beyond me. It's been abandoned for fifty years."
"It doesn't matter," Robotnik dismissed, taking the Egg Walker to the transporter. "Shadow promised big rewards and I plan to take them."
Robotnik was then instantly transported away, with all the robots unaware of a winged figure watching from afar.
…
High up in space in a secluded and forgotten Space Station known as the ARK, Shadow stood and waited in a room with a large pillar containing seven empty slots in front of a computer console. He finally cracked his eyes open and smirked as Robotnik entered the room.
"I've been waiting for you, Doctor," Shadow greeted as Robotnik exited the Egg Walker.
"I didn't mean to keep you waiting. It just took longer than expected to create a functioning space transporter. Not all of us can manipulate Chao Control like you can."
"A gift from your late grandfather. But now, I will show you the greatest achievement of the late Professor Gerald Robotnik."
Shadow then turned to the console and pressed a few buttons, causing monitors to turn on and machines to power up.
"The ARK was the first space colony created by mankind. A means to live in and explore space, looking for mysteries that would aid all mankind. What the public didn't know was that the ARK also contained a top secret research facility, where weapons of mass destruction were being created." He gestured to the device behind him. "This is one of them. An ionized laser energy beam capable of destroying an entire planet. Codenamed: the Eclipse Cannon!"
"Destroy an entire planet? Grandfather was bold."
"That's only at its most powerful," Shadow told him. "Unfortunately, it's been deactivated for quite some time now."
Shadow then took out his green Chaos Emerald and tossed it into one of the slots on the machine, causing a surge of energy to course through it.
"To reactivate it, large amounts of energy are necessary."
"So that's where the Chaos Emeralds come in."
"Exactly. We will need all seven Chaos Emeralds to power the Eclipse Cannon. Once you have them, you will have the ultimate weapon in the universe to use as you please. And then… the world will be yours."
Robotnik cackled wildly in response, much to Shadow's delight.
"This is perfect!" Robotnik cheered. "With this kind of power at my disposal, I'll be able to conquer the world a hundred times over. The Robotnik Empire is soon at hand!"
"That's all well and good, but do you honestly think it'll be that simple?"
Everyone turned around, shocked to see Rouge hanging upside down from the ceiling. She flipped over, landing on the ground before them. She had Kat's bag dangling from her shoulder, a fair sized bulge suggesting it wasn't empty.
"I remember you," Robotnik told her. "What are you doing here?"
"I've come to make a deal," she replied. "You see, I'm trying to find something rather important."
She reached into the satchel, pulling out a shard of the Master Emerald.
"So, that big rock Knuckles cares so much about is shattered again?"
"Yep. The big lug's got that built in radar of his, so if I want to find the pieces first, I need an edge. Thus, I'm here for a trade. You provide me with the means to track the Master Emerald Shards, and I'll give you the Chaos Emeralds."
To prove her point, she pulled out the blue Chaos Emerald, holding it out to him. Robotnik turned to Shadow who nodded in response.
"Alright batgirl, you've got a deal."
Rouge smirked, tossing the Emerald to Robotnik before her eyes fell on Shadow.
"Why hello there. I don't think I've ever seen you around Mobius. You new to town?"
"You might say that," Shadow replied.
"The name's Rouge. Rouge the Bat. And you are?"
"... Shadow. Shadow the Hedgehog."
…
Meanwhile on Prison Island, Sonic was locked up in a specialized chamber that was placed in an underwater room, making escape tricky if not impossible. Sonic just sat against the only wall of his cell, mulling over the day's events.
"What a day. One minute I'm the hero, the next I'm public enemy number one. Since it doesn't look like I'm going anywhere anytime soon, better use my time wisely. Maybe figure out who that Shadow guy is, and what he wants."