Shadow was standing in a field, his arms crossed. A piece of paper blew by, sticking onto his leg for a moment before blowing away. He didn't notice it as his attention was fixed on Westopolis.

FIRE IN THE SKY FESTIVAL* Celebration! 50 Year return of Black Comet.

'Shadow the Hedgehog... Why does that name haunt me? It's the only thing I can remember. And that gruesome image...' he thought then cringed as she squeezed her eyes shut to remember as she saw a memory of Maria.

Maria was desperately running down a corridor of the Space Colony ARK before turning back to see a squad of GUN soldiers stop upon reaching a doorway some distance behind her, all of them equipped with various firearms such as assault rifles, sub-machine guns, and a pistol. Maria turned to look helplessly at someone next to her with a frightened gasp. Then the lead GUN soldier raised his pistol, took aim, and shot her. Then the gunshot was heard.

"Maria!" Shadow said echoing.

Then he snapped back to reality.

"Who am I... and why can't I remember anything? And who is this Maria?" he said and a dark cloud loomed over him.

He looked up towards it as several clouds gather over Westopolis around some sort of opening in the sky. Thunder crackled and rumbled as lightning flashed within the clouds, while the opening has a white glow from its center. As the clouds circled the opening for a few seconds, then a bunch of Black Arms fallout from the opening and began laying siege to the city. It then shows a stronger Black Arm which crushes a car as it lands, then smashes another one that drove by with a feral snarl, sending it flying towards a building on the opposite side of the street.

Back in the park, Shadow watched the carnage with disgust and distaste.

"Hmm, look how pathetic they are! I don't have time for these humans." he said.

"Shadow..." someone said and he stopped in shock and surprise before turning around as his eye came floating in toward her, projecting an image of Black Doom. "As you can see, the day of reckoning will soon be here. Find the SEVEN Chaos Emeralds and bring them to me as promised."

"Huh? Who are you and how do you know I'm Shadow? And what are you talking about?" Shadow asked and Doom's Eye ended the projection of Black Doom and flew away.

Before he could follow, a ton of explosions occur near him, preventing him from pursuing Doom's Eye as they pocket the area around him with blast craters. Once the smoke cleared, he was unharmed, but puzzled by what she just heard.

"Just what was that all about? If he says he knows the truth about who I am... then like it or not, I have to believe him. The only way I'm going to get the secret of my past is to get those Chaos Emeralds!" he said and ran off into Westopolis."

At G.U.N. command center the Black Arms were on the various screens, as well as a map of locations around the world that had been attacked by the Black Arms. A soldier ran up to Towers, watching events from his chair in the back of the command center.

"The black aliens have hit six major cities around the world, and every city is reporting significant damage and casualties. Among them, Westopolis has received the heaviest casualties due to its weakened defense system. Downtown Westopolis has been almost completely destroyed. Unconfirmed sources have also reported seeing a black hedgehog in Westopolis." Captain said.

"Shadow? Deploy the troops, NOW! And if you find Shadow with the black aliens, then kill them all!" Towers said.

"But sir, isn't Shadow on our side... sir?!" Captain asked rubbing his helmet in confusion.

"I gave you an order, soldier! He's evil and he's the enemy!" Towers said and Captain left the room. "You can't fool me, Shadow!" he said clenching his fist. "This time, you're MINE!"

At Westopolis. Shadow was holding the green and blue Chaos Emeralds when Sonic came running up.

"Now that was sweet, Shadow!" Sonic said.

"Yeah... Well I'm not here to save you!" Shadow said.

"Thought you might say something like that! How about a little friendly competition?" she asked and he turned from her.

"Don't waste my time." he said whenever a Doom's Eye floated up and turned to face him.

"We've found the THIRD Chaos Emerald in this city. Our mission here is done. Now get going!" Black Doom said and floated off.

"Guess that means... welcome to the next level. Let's go!" Sonic said and ran off.

"Get back here!" Shadow said and followed her.

Later at Lethal Highway Shadow and Sonic came running in towards Doom's Eye, who turned to look at them.

"Hand over that Chaos Emerald or else!" Shadow said.

"So... think you have a chance against ME... do you?" Black Doom said.

"Look...I don't take orders...especially from you. But I'm not here to fight you, either. I'm collecting the Emeralds to find my own answers. So why don't you just back off?!"

"You still don't know your place, do you? BLACK BULL! I summon you!" Black Doom said and the Black Bull appeared. "Behold! The wrath of Black Arms!" he said and Black Bull roared.

"Woohoo! Now we're talking! Bring it on!" Sonic said.

At the President's office in the White House.

"Mr. President. We've received a report from the Central Information Agency. Our ground troops have successfully pushed back the black aliens from Westopolis. We've also managed to suppress alien forces in five other cities. There's also reports that the CIA's mainframe has been compromised. We're investigating the incidents now. It is a strong possibility that this was also committed by the black aliens." secretary said through the phone.

"Tell the Commanding Generals that the United Federation will never surrender to terrorists!"

"Yes, Mr. President." secretary said through the phone and the President looked at picture of Sonic and Shadow.

"This planet was once saved from tyranny and annihilation by you two heroes. Now mankind must protect this peace... at all costs." he said looking out window over Central City. "We must stand united to defend our world against these invaders!"

Later Shadow was running to Circus Park.

"Where's that damn FOURTH Chaos Emerald!?" he said and looked up to see Tails flying in the Cyclone. "Hey isn't that... Tails?!"

"Look at that! It's Eggman's theme park. He made it out of the Rings he's taken from around the world. I've got to get those Rings back!" Tails said.

"A Chaos Emerald!"

"Whoooaaa!" Tails said and the Cyclone flew out of control due to the fireworks.

"This is just too easy. Guess it's my lucky day!" Shadow said and continued running to the park's entrance.

At G.U.N. headquarters. As the command center continued tracking their forces engaged with the Black Arms around the world, Towers continued watching things from his chair at the back of the room before an alarm sounds and the G.U.N. Captain from earlier entered and salutes as he gave his report.

"Commander! COM Sector B3 are reporting that the black aliens have successfully been driven out of Westopolis. We've contained them in the forest and they're completely cut off from the rest of their support." Captain said.

"Well done, Captain. What about Shadow?" Towers said.

"Sir! We think Shadow escaped into the forest with the black aliens."

"Alert all field commanders in Sector B. I'm authorizing full use of all tactical weapons. I want both black aliens and Shadow stopped and buried. Failure is not an option."

"Yes sir!" Captain said and left to relay Towers' orders.

After he left, Towers chuckles to himself with satisfaction.

"Hmm, hmm... It's over, Shadow. You will finally be exposed and eradicated for the evil that you are!" he said and kept looking at the command center as the map in the center of the far wall pinpoints the location of Shadow and the Black Arms.

Doom's Eye hovered over a platform as Shadow approached to confront it once more.

"Having a little trouble with those GUN agents... are we?" Shadow asked.

Meanwhile Rouge was overhearing the conversation from a nearby ledge.

Black Doom chuckled.

"What a pitiful bunch..." he said.

"What'd you say?" Shadow asked.

"We're not here to exterminate these poor creatures. On the contrary..."

"Wha... what is he talking about?!" Rouge asked.

"What are you saying?" Shadow asked and Black Doom chuckled.

"All will be revealed... tomorrow." Black Doom said.

"Tomorrow!?" Rouge said to herself shocked.

"Shadow, you should rest. You need to be ready for tomorrow's ritual." Black Doom said and the Black Bull rise from behind as Doom's Eye floated away.

"You scum! You're going down!" Shadow said and Black Bull roared.

Later at Iron Jungle Shadow warped into another part of the forest. A shuttle-like machine flew up next to him, which Sonic was standing atop of.

"What's up, Shadow?" Sonic asked.

"Not you again..." Shadow said.

"Nice to see you too. Looks like those black creatures are headed out to space. We're on our way to the ARK, so I guess that means we're going too."

"ARK..."

"Come on, let's roll. Next stop, the ARK." she said and he stepped inside the machine, which rev its rocket engines and flew off.

The shuttle was in space, with the ARK in view. Shadow looked at the cyan Chaos Emerald, which in a glass case powering the engines.

"A Chaos Emerald? You've gotta be kidding me, guys! This is like taking candy from a baby, which is fine by me." Shadow said, punched the glass and grabbed the Chaos Emerald.

An alarm begins to blare and red lights start flashing. Shadow looks out the window. and hears Maria in his mind.]

"Shadow! Help me!" Maria said.

Then Shadow saw himself on the ARK 50 years ago.

"Maria?!" Shadow said.

"Please, Shadow," Maria said and ran up to Shadow. "I need your help! My grandfather's experiments... something's gone horribly wrong!"

"What is it?"

"The research lab... it's going to be destroyed. Something must be done! Please Shadow, I beg you! Help Grandfather and those aboard the ARK! Please!"

"I'll be there, Maria." he said and raised his fist. "I swear, whatever it takes, I'll take care of the ARK and the professor!"

Later Shadow had a vision of Maria just after she had been fatally shot by GUN soldiers.

"Maria!" Shadow said.

"Please, Shadow... I need your help! Everyone's fate depends on... YOU!" Maria said.

"MARIA!" he said and the escape pod was shot from the ARK and plummeted towards Earth.

Later Shadow and Sonic made their way through the ARK.

"Maria..." Shadow said and Sonic noticed something.

"Shadow! Look... up there!" Sonic said and he snapped back to reality.

"Huh?" he said and the Black Comet roared overhead. "What is that?"

"Once every 50 years, that Black Comet passes by this planet." she said and chuckled. "Oh! Do you think those black creatures are somehow connected with that comet?"

"Black ... Comet" he said and fell to his knees, clutching head in pain. "UGH!"

"Shadow! What's wrong?!" she asked alarmed.

"I think you're right... I feel it... they're up there. That's where the answers are... I've got to get to that comet!" he said and they ran off to Tails' spaceship.

Later Shadow and Sonic approached Black Doom.

"You've done well, Shadow. I'm very impressed you've made it this far..." Black Doom said.

"Black Doom! Your rule ends here and it ends now!" Shadow said.

"So you're behind all this!... Like it or not... the game's over!" Sonic said and Black Doom laughed.

"Fools! The Black Arms are more than superior... we are perfect! Do you really think you have any real chance of defeating us?" he asked and laughed. "Hahahaha..."

"It's you who should be scared, Black Doom! I made a promise to Maria to save the planet she loved so much... and I WILL!" Shadow said

"Then get ready to die! Let me show you THE ULTIMATE POWER IN THE UNIVERSE!"

After the fight Black Doom lay on the ground in front of Shadow, defeated. Shadow reached for the red Chaos Emerald as the other six flew around him, while Sonic stood next to him in triumph.

"Finally... I've got ALL the Chaos Emeralds!" Shadow said

"Shadow! This isn't over yet! The Black Arms will rise again..." Black Doom said breathing heavily.

"Let's do this!" Sonic said and fought the want to take out her guitar.

"I'm Shadow the Hedgehog, and I made a promise that I intend to keep! With the power of these Emeralds, Black Doom and his army are finished! THIS IS WHO I AM!"

Above the surface of the Earth in space, was the Black Comet. Then it blinked out in a green light and appeared again on the surface of the Earth, above a city. The Black Comet then shot out roots burrowing into the planet.

Inside the Black Comet.

"What was that? What just happened?" Amy asked.

"Those black creatures just warped the comet down to the surface using Chaos Control!" Sonic said.

"No! That's impossible!" Rouge said.

"That's why you needed the Chaos Emeralds." Shadow said

"Hahahaha... precisely. The comet's velocity isn't powerful enough to pass through another planet's atmosphere. The Emeralds amplify the space-time control powers of Chaos Control. We need them to charge to full power. It's the perfect plan. That's why I needed the professor to help me..." Black Doom said.

"What?!"

"That's insane!" Eggman said.

In a flashback Gerald Robotnik and Black Doom were on the Space Colony ARK near a tube with Shadow inside it.

"The professor was in development of the ultimate life force but he needed my help. So we made a deal... I helped him and he promised to deliver me the SEVEN Chaos Emeralds. That's how you were created, Shadow. You would help us do both!" Black Doom said.

"Me!? I can't believe it!" Shadow said and knelt down in shock.

"That can't be! He betrayed his own people for research!? For Black Doom?" Eggman said.

"Big deal... we can't just stand here doing nothing!" Sonic said.

"Yeah... let's do this! I'll crush that cosmic rock ball!" Knuckles said and struck a pose, but then stopped moving.

"Knuckles! What's wrong? Ughhhh!"

Suddenly, all the visitors to the Black Comet stopped moving.

"A special weapon... this gas, once released is quickly absorbed into your blood stream. In a moment, total paralysis will hit your nervous system. The end is near, now. Hahahahaha..." Black Doom said and summoned the Death Leeches. "Ahhh... my dear offspring... Eat and devour these savory dishes!" he said and the Death Leeches moved in on the paralyzed victims.

Many of the others yelled at them unable to fight back because of the paralysis from the gas.

"Help me! Stop it! Back off, you slimeballs!" Sonic and the others said while Shadow remembered his journey.

"I will avenge those whose blood has spilled!" Towers said.

"Did I... die?" Shadow asked.

"That's why you were created..." Black Doom said.

"Please help me, Shadow." Maria said.

Then Shadow opened his eyes and stood up, spotting a Death Leech and abruptly stomping on it.

"What?" Black Doom asked.

"I am Shadow the Hedgehog. I've left the past behind me. No one can tell me what to do now! I will destroy you, Black Doom!!" Shadow said

"I gave you life and THIS is how you repay me! The irony of it all is... I gave you life... NOW I'll take it back! Hahahaha..." Black Doom said and left with Shadow following.

"Shadow..." Rouge said.

"You're our only hope now!" Sonic said.

Meanwhile Shadow reached Black Doom.

"Well done, Shadow, You've gone farther than I expected... I'm impressed!" Black Doom said and Shadow walked towards him. "But you still don't understand, do you? The future we offer is the only option for these humans."

"I've heard enough! You're boring me to death, Black Doom! You're going down!" Shadow said and Black Doom laughed.

"Such bravado for a little hedgehog! I thought you were different from the rest... but maybe not. We are more alike than you think... the same blood runs through our veins."

"This can't be... Uugghh..." Shadow said lutches head in pain and falls down. "Just... who are YOU?"

"Don't you know? You were created from my blood..."

"Wha... what!?"

"That's right... You are a part of me... do you feel that? I can control you... You cannot escape me... nor can you escape your past! Hahahahaha..."

"Damn you! NO, it's not true!"

Onboard the ARK Team Chaotix was hacking the ARK's database.

"Espio... are you in yet??" Charmy asked and Vector pushed him away.

"Quiet, Charmy! Espio, we need you to focus 'cuz if we don't hurry all the data we recovered will be lost." Vector said.

"Easier said than done... who signed me up for this anyway?" Espio said.

"That's it... I'll do it... get out of the way!" Charmy said.

"Get back here you idiot!" Vector said and Charmy hit the computer very hard, causing it to work.

"Hey it's working!" they said and the computer showed a video of Professor Gerald Robotnik.

Inside the Black Comet.

"Shadow, my son." Gerald said.

"Professor...?" Shadow said.

"What is this!" Black Doom asked.

"If you're listening to this then the worst has happened... you need to know the truth. The government plans to shut down this research facility." Gerald said.

Inside the headquarters of GUN.

"The government plans to cease all of our research... and imprison all who know about you. I made a terrible mistake, Shadow. It's all my fault... making contact with that comet." Gerald said.

"Professor Gerald...?" Towers said.

"Now, listen very carefully..."

Inside the Black Comet Sonic and her friends were still paralyzed.

"In 50 years, the Black Comet will return... they plan to harness its powers to destroy this planet! The only way to stop them... was to develop a way to use the very power they intended to use against them." Gerald said.

"That's it! It's brilliant!" Eggman said.

Inside the Black Comet, in front of Shadow and Black Doom.

"Shadow... it's up to YOU and only YOU can stop them! I developed the Eclipse Cannon... It's the only weapon that can destroy that Black Comet. Shadow, you are the only hope... to save mankind as we know it. The future of this planet depends on... YOU!" Gerald said and Maria entered the video.

"Don't worry, grandfather. Shadow and I will protect this planet. Right, Shadow?" Maria said.

"Gerald.. you fool!"Black Doom said and the videos disappeared on hiss order. "Shadow is already in my control... What's this?!" he said and Shadow stood up. "Well, well, well... seems like you're immune to my mind control."

"You have no control over me, Black Doom! I now understand why I am here... I made a promise and I'm here to keep it! Today, I put my past behind me!" Shadow said and and leapt up to kick him, but he disappeared while leaving the Chaos Emeralds behind.

"Have it your way, Shadow. So be it... be prepared to meet your maker! Your past, present and future ends here... TODAY! Prepare to die! Say goodbye Shadow as you witness my true wrath!"

Then Shadow used the Chaos Emeralds to become Super Shadow and flew out of the Black Comet.

When he got there he stood on top of the Black Comet.

"Only one thing left to do..." he said and flew to the bottom of the Black Comet. "To put the past behind me!! Chaos... Control!!" he said and teleported the Black Comet into space.

Then the Eclipse Cannon opened and fired at the Black Comet, shattering it to pieces.

In Westopolis, Sonic and her friends watched the Black Comet's destruction.

"YEAH... He did it! The Black Comet is destroyed!" Tails said.

"Shadow... That was SWEET!" Sonic said.

"I hope he's OK." Rouge said.

"I'm sure he's fine, Rouge. After all, he is Shadow!" Amy said.

"How about giving me back those Chaos Emeralds now?" Eggman asked.

"Hey, get back here you creep!" Knuckles said and started chasing after him while the others watched, laughing.

Inside the GUN's headquarters. G.U.N. personnel at the various consoles were raising their arms and cheering in victory as the monitors show the destruction of the Black Comet and the end of the Black Arms and their invasion.

"How ironic... After the way we all treated him, he save us all in the end. We were all wrong about the professor." the president said but got no reply. "Let us pay homage to Professor Gerald. Let's work to ensure peace and prosperity for a brighter future! What do you say, Commander?"

"Excellent idea, Mr. President." Towers said.

Inside the Space Colony ARK, Shadow was holding an old picture of Maria and Gerald Robotnik.

"Goodbye forever... Shadow the Hedgehog." he said and threw away the picture while walking away.