A GUN military helicopter was flying over Station Square and Sonic was a prisoner onboard the craft.

"Attention, Control, we are currently heading south. Suspect is in custody." Pilot said on the radio.

"This is Control speaking. We've verified your position. Handle suspect carefully. He's a slippery little guy." Mission Control said over the radio.

Sonic was handcuffed and sitting between two GUN soldiers.

"You're awful quiet." a Soldier said.

"So what?" Sonic asked.

"Well, from what I heard, you've caused quite a ruckus over at Prison Island the other night. Now we can't get two words out of you."

"Guess I'm not feeling too chatty."

Another soldier stood up and menaced him with his gun.

"You better watch that smart mouth, hedgehog, or you'll be running laps in a ten-by-nine cell."

Suddenly Sonic created a ruckus on the chopper.

"What's going on up there?" Mission Control asked over the radio.

Then Sonic emerged from the helicopter and landed on the stabilizer wing.

"I gotta get the chump on these fly guys." Sonic said.

"Hey! What do you think you're doin'? Come back!" the soldier said.

Sonic sawed off the stabilizer wing and rode it down toward the city. He landed in a skating rink, rode it across a half-pipe, and ditched it.

"Sorry, dudes!" he said.

At GUN HQ. "Suspect located!" Officer said.

"Deploy robots immediately!" another said.

"Roger!" another said.

In Central City Sonic reached the top of a hill on one of the roads, only to be met with a swarm of GUN Beetles that force him to run in opposite direction.

"I am outta here!" he said and dodged their laser damaging stoplights, cars, and even buildings. "Uh-oh. They mean business!" he said and ducked down a manhole while the Beetles flew past.

Soon he was walking through the sewer.

"Could I possibly sink any lower?" he asked. "What am I running away from, anyway? I mean, I haven't done anything wrong, have I? I just wonder what it is they think I did..." he said to himself.

Elsewhere Chris was walking in the sidewalk with another kid.

"Hey Chris, I heard you come from Station Square." a kid said.

"Uh... Yeah?" Chris said.

"Have you ever seen Sonic the Hedgehog up close?"

"Uh... Sonic? Well... sorta."

"What's he like? Is he really that fast?"

"You bet he's fast! He's faster than anybody, and he's nicer than anybody, too."

"Wish I could meet him. Heh, who knows, if we're lucky, maybe we'll both get to meet him someday."

"Well, I gotta get to class. Later!"

"See ya!"

As the kid left, Chris looked skyward.

In the President's limo Christina Cooper was reading a report.

"Mr. President, it appears our undercover operative has settled into his new mission and will have all of the resources necessary." Christina said.

"Good work. And what about the flood?" the president asked.

"Well, sir, I've read the full report over the last few days. There was some damage, but from what I can gather, none of the citizens were harmed in any way."

"And what about Sonic? Is there any new information?"

"I'm afraid it doesn't look good, and with a crime of this magnitude, sir, I'm not sure the government should get involved."

"I don't know. This just doesn't sound like him."

"I agree with you, sir. Sonic would never do such a thing. I think he's been wrongly accused, Mr. President, and I think you should do something about it." Sam said.

"Just drive."

"Either way, I don't feel it would look good for us to be involved. We should wash our hands of him." Christina said.

"Do you really think so?"

"I do, sir."

Suddenly Sam slam med in the brakes, throwing her into the glass.

"Are you crazy?! What are you trying to do?" she asked.

"I'm trying to do my job. Just driving." Sam said.

That night, the mysterious hedgehog showed up at the National Museum in front of an exhibit containing a Chaos Emerald. Immediately the alarms sound, and the hedgehog ran out, only to be met by several GUN Beetles. They fired at him, but he smirked and nimbly dodged them. Then he used a powerful energy destroying the Beetles as he made his getaway.

At the White House.

"Mr. President, I have some bad news. Sonic was just seen at the National Museum of Art attempting to steal the Chaos Emerald." commander said.

"It can't be." the president said.

"My men are awaiting your instructions, sir."

"We have no choice. Find him and place him under arrest."

Commander saluted.

"Yes, Mr. President. I'll alert all divisions immediately, sir." he said and left.

At GUN Headquarters.

"Attention all division commanders! Sonic the Hedgehog has gone underground. Let's go get him." Commander said.

Then a swarm of GUN Beetles took off into the night sky.

At the Thorndyke's apartment Chris, Chuck, Ella, Tanaka, Cream, and Cheese were watching the news.

"And now a breaking news story. I'm standing in the main pavilion in the Nation Museum of Art, where earlier tonight, a thief broke through security and stole a priceless Chaos Emerald. Authorities found these images on tapes confiscated from the museum's security cameras." News Reporter said.

The camera footage showed the mysterious hedgehog breaking the glass surrounding the Chaos Emerald. He appeared in front of the camera and grinned before making his getaway.

"Was that Sonic?" Chris asked.

"It can't be! Sonic would never take something that doesn't belong to him!" Cream said.

"Chao chao chao chao chao chao!" Cheese said.

"Yeah, right. That was Sonic on those security tapes." Chuck said.

The others became mad at him.

"It can't be!" Chris said.

"He was framed!" Ella and Tanaka said.

"That's right!" Cream said.

"Chao chao!" Cheese said.

"Uh... Maybe it wasn't him. I guess you can't always believe your eyes." Chuck said.

"Surprisingly enough, authorities have determined from this footage that the thief is none other than Sonic the Hedgehog. According to reports, Sonic has destroyed numerous government tanks and fled to an unknown location." New Reporter said.

"But there... there must be some kind of mistake. Sonic wouldn't..." Chris said and sighed.

"Of course he wouldn't, Mr. Chris. I'm sure there are some explanations." Ella said and Tanaka nodded.

Chris walked over to the window and looked up at the sky.

"Sonic... What's happening?" Chris said to himself.

At Central City the GUN Beetles blew up various sewer entrances and flew in.

In the sewer Jerome and several other poor men were huddled around a fire.

"What, are you crazy or somethin'? Sonic ain't no thief." a man said.

"I wouldn't make this up! I saw it on a TV in a repair shop window. Would I lie to you? No. I tell you, they saw him steal the thing." Jerome said.

"Hey!"

"And not only that, they caught him breaking into Prison Island just last night - red-handed. Probably trying to steal government secrets."

Sonic ran past them, with several GUN Beetles in pursuit.

In Prison Island Mr. Stewart drove Scarlet Garcia up to a security checkpoint.

"How did you manage to get permission for me to visit Prison Island?" Scarlet asked.

"Well, let's just say I have connections in high places." Mr. Stewart said and

Mr. Stewart showed his credentials to the camera then the doors in front of the car open, and the drove through.

"Who are you, exactly?"

"Just a fellow news hound, that's all."

Once inside, they interviewed the warden.

"Have you ever heard of a government operation called Project Shadow?" Scarlet asked.

"I'm afraid that's top-secret. However, after last night, I'm not sure how much longer it will stay secret. Take a look." Warden said and

The warden showed them security footage of Eggman giving the mysterious hedgehog the order to destroy a GUN robot.

"This is security cam video from last night. As you can see, Eggman and the hedgehog have broken into the system, and are trying to steal the Project Shadow file." he said and the footage ended.

"This video tape makes it clear as day. Sonic is no longer concerned with the safety of our citizens, and had decided to join forces with the enemy. He had us all fooled, didn't he?"

"What happens next, sir?" Mr. Stewart asked.

"Quite simple. We arrest him and try him for high treason."

A still of the mysterious black hedgehog was shown.

At Central City Sonic burst out of the sewer, then used the manhole cover to dive down and destroy the GUN Beetles.

After the Beetles were destroyed, Sonic put the manhole cover back.

"That was easy." he said then spotlight blinded him as a Big Foot landed nearby. "Can't hang around, big guy, sorry. I'll give you a ring some time, what do you say?" he said and held up a Power Ring, but the Big Foot started firing at him and he easily dodged. "Now that's what I call a tight squeeze."

Then he activated the ring and home attacked the spotlight, destroying it.

The Big Foot reacted by firing eight missiles at Sonic. Sonic allowed to chase him up a building, then he landed on the Big Foot and jumped off, causing the missiles to destroy the robot.

"That guy's gotta work on his aim a little bit." he said.

Then a glow came from the destroyed robot.

Then the glow subsided, revealing the mysterious black hedgehog.

"What the...?"

"Good evening. I must say, it's a pleasure for me to finally meet you face-to-face, Sonic. We do look alike. It's uncanny." the hedgehog said.

"Wait a minute! So it's you who been getting me into all this hot water lately! Impostor!" Sonic said and leapt toward the robot to attack the hedgehog, but he vanished before Sonic got there.

At Prison Island Mr. Stewart was looking at the still of the hedgehog.

"It certainly looks like Sonic... but still, there's something strange, different about him." Mr. Stewart said to himself.

Back at Central City Sonic looked up to see the black hedgehog atop a building.

"I assure you, Sonic, I'm no impostor. I possess too much power to be anything but the real thing." the hedgehog said.

"Well, if you're so powerful, let's see you prove it!" Sonic said and ran up the building, but the hedgehog faded before he could get there.

He saw the other hedgehog atop a taller building and laughed.

"Hey, not bad. I'm almost impressed. How about a little race action?"

Soon Sonic was racing the other hedgehog through the city. Notably, while Sonic was running, the other hedgehog appeared to skate.

At the apartment Chuck was on the phone.

"You're kidding! Unbelievable. Well, be sure to call us right away if anything else happens." he said and hung up. "That was your father. Apparently Sonic's been spotted battling a government robot on downhill street."

Chris instantly got up and ran out of the room.

"Chris, where are you going?" Ella asked.

"I will follow him, Mr. Thorndyke." Tanaka said and left.

"Slow down! I'll come with you." Chuck said and left to.

Back in Central City the hedgehog cut in front of Sonic.

"He's tougher than I thought he was." Sonic said to himself.

"Not quite." he said and caught up.

Tanaka was driving Chris and Chuck into the city when they saw Sonic and the other hedgehog running toward them. The black hedgehog vanished, and the car skid to a stop. The other hedgehog reappeared and kicked Sonic to the ground.

"What just happened?" he said.

Then a spy drone showed up.

At Eggman's base.

"Sonic's a bit overwhelmed, isn't he? I certainly can't blame him. I felt rather confused myself when I encountered Shadow for the first time." Eggman said.

In a flashback Prison Island after activating the Project Shadow machine, Eggman watched as the black hedgehog rose from his stasis chamber.

"What?! It's that hedgehog! How dare you deceive me, you speedy little slimeball!" he said and

The hedgehog climbed out of the chamber.

"Wait. You're not Sonic."

The hedgehog bowed. My name is Shadow. You've awakened me from a state of suspended animation, and I am very grateful. To show my gratitude, I am at your command." he said.

Then a GUN Hot Shot burst into the room.

"Bad timing as usual!" Eggman said.

"Wait. I will show you my power, Doctor." Shadow said and attacked and destroyed the robot.

Back in Eggman's base.

"You've met your match, Sonic! Compared to Shadow's fancy footwork, your as slow as a man of molasses! And now that you two have gotten a bit better acquainted, you're sure to see that for yourself!" Eggman said and laughed. "After sixteen long years I've finally won!"

Back at Central City Shadow stood over a fallen Sonic, Chaos Emerald in hand. Then he held it up.

"He's got a Chaos Emerald!" Chris said.

"Where'd you get that Chaos Emerald, you phony freak? Hand it over!" Sonic said. "They only work with me. You need my permission."

Shadow teleported behind Sonic.

"You can do better than that, Sonic. If you don't light a fire under those feet, you'll never get this Emerald back." Shadow said. "Even if you are the guardian."

Sonic leapt into the air, and attempted to kick him, but he teleported again.

"He really is faster than I am!" he said shocked.

"But that's not speed. He's disappearing!" Chuck said.

"Whoa!" Chris said.

Shadow was now on top of a street lamp.

"That's not all. I'm full of surprises." Shadow said.

"Grandpa!"

"Chaos Control now." Shadow said and activated Chaos Control while Sonic ran.

"He can cause Chaos Control with just one Chaos Emerald? Who is he? And there did he come from?" Sonic said to himself.

Then he remembered something.

'They will help them and in reward be able to use something no one else can do but one other person with their permission.'

"He has to be the other person! He just doesn't know what exactly he has to do with the Chaos Emeralds unlike everyone else!" he said.

Then Shadow reappeared next to him and delivers blow after blow.

"Leave him alone!" Chris said.

"Like to fight dirty, don'cha?"

"Consider yourself fortunate. If I'd used my full strength, you'd have been much worse off than this." Shadow said and overshadowed Sonic. "Many years ago, Professor Gerald Robotnik endowed me with the power of Chaos Control. A normal creature like yourself doesn't stand a chance against me."

"Don't underestimate us "normal" types."

'I know plenty of things about him. I just didn't know he had a grandfather.' he thought.

Shadow glanced up for a moment, hearing the sound of the approaching authorities, then looked back at Sonic.

"I have a feeling I should make myself scarce. Goodbye, Sonic. It certainly was a nice pleasure. Chaos Control now." he said and used the Chaos Emerald to vanish as several police cars, helicopters, and GUN Beetles arrived.

"Sonic, we've got you surrounded! You're under arrest. Put your hands up!" a police officer said.

"No way! You can't arrest me! I didn't do anything! Honest!" Sonic said.

Among the officers wa Officer Albright.

"I'm gonna give you to the count of five to surrender! Ready? One... Two... Three... Four..." Albright said.

"Turn yourself in, Sonic! You're already in trouble. Just do as they say!" Chris said.

"Please, Sonic..." he said with tears springing to his eyes.

"You're time's up, buddy! We've got a special cell on Prison Island with your name on it!"

"Did you just say Prison Island?" Sonic asked.

"Yeah, what about it?"

"Really, you mean that's where you're taking me from here?"

"That's where we usually take criminals."

"Okay, Chris, I'll do it. I'm gonna turn myself in. [to the officers] All right, guys, cuff me. I'm all yours." Sonic said and sat cross-legged.

"Get him!"

"Only just take it easy on the wrists, fellas." he said. "You might use Chaos Control, friend, but I'm gonna have to get out of this without tricks. I'll do it... somehow. And when I do, we'll meet again." he said to himself and was led in handcuffs to a helicopter. "Don't worry about me, Chris. I'll be out before you know it, buddy!"

"I hope so..." Chris said teary.

The helicopter took off and Shadow watched from a distance.

"I won't let anyone stand in my way. Least of all you, Sonic. Maria..." Shadow said to himself.

At Eggman's base Eggman and his hench-bots were celebrating their victory with Shadow.

"Yippee!" Eggman said.

"We did it! We did iiiit!" he said and shook Shadow's hand. "That hedgehog's in the hoosegow thanks to you, Shadow!" he said. "And finally after sixteen years he's lost!"

"He is practically busting his buttons." Decoe said.

"That jacket always was tight around the tummy." Bocoe said.

"Remember, Doctor, you must still obtain five more Chaos Emeralds in order to use the Eclipse Cannon. But when you do, it will give you ultimate power and make you master of the universe." Shadow said.

"Sounds good to me! And now to has out the rest of our dastardly strategy. Let's see..." Eggman said.

Then Bokkun flew in holding his TV.

"Doctor, I have a message for you this time!" he said and gigled then tossed the screen to Eggman, and it activated.

Rouge was holding a bouquet of roses.

"Hiya, Doc. Long time no see. I was wondering if we could get together to discuss a little business transaction?" Rouge said.

"A business transaction?" Decoe said.

"I would not trust her, Doctor." Bocoe said.

"Who asked you, bolt-brain?! Fetch her right away!" Eggman said.

"Uh-oh!" Decoe said.

"Here we go!" Bocoe said.

The outside of the pyramid base was shown while the TV explodes. Bokkun laughed.

"That's not funny!" Eggman said.

"Don't blame me! Lots of stuff have television bombs!" Bokkun said.

Rouge dropped in still holding her roses.

"I just hope this little scam of mine works." she said.

"Oh! I didn't expect you so soon." Eggman said.

"Good evening, Doctor. I've got a little something I'd like to show you." she said and showed him the blue Chaos Emerald she acquired at Angel Island.

"A Chaos Emerald..."

"It's all yours, Eggy, if you agree to my conditions. All you have to do is be a good boy and play nice, and I'll tell you where the others are. What do you say, Doc? Do we have a deal?"

Shadow scoffed.

"That depends. What do you want?"

Shadow started to see a vision of Maria.

"Pleasure before business. Who's this charming friend of yours? I'm Rouge the Bat. What's your name?"

"It's Shadow." Shadow said and turned to her face. "Shadow the Hedgehog."

Rouge was startled by Shadow's ruby red eyes.

At the harbor Chuck, Ella, Cream, and Cheese watched as Tanaka and Chris boarded a ship dressed in black outfits and hats.

"Don't worry, you guys. We'll be back soon. But... this is something I have to find out for myself." Chris said.

"We understand, Chris. You two take care of yourselves." Chuck said.

"Why do we have to dress like this, Mr. Tanaka?

"I've been inspired by my boyhood hero." Tanaka said.

Meanwhile Tails and Amy were on the X-Tornado also on the move. Amy was impatient.

"Come on! Step on it! We've got to get to Prison Island in a hurry!" Amy said.

What a bossy-" Tails started.

"What did you say?"

"Uh..."

At Prison Island Sonic was sitting alone in his chamber. It was surrounded on all sides by water, making it practically escape-proof. There were various mathematical formulas on the walls.

"What a day... Who'd have thought I'd be thrown in jail for something I didn't do? I'd better think fast, use my time wisely, and figure out who that Shadow was, and what he wants." he said to himself.