Rouge was at the ARK Colony sitting inside a shuttle, speaking to Topaz over radio.
"Topaz, I'm transmitting my report now. Over." Rouge said on the radio.
"Be careful, Rouge. That space colony is a dangerous place." Topaz said over the radio feeling the ground shake as the ARK descended."
At the Eclipse Cannon Sonic and Shadow were still fighting creating a hole in the wall, revealing a Power Ring.
"You've interfered for the last time!" Shadow said and threw more Chaos Spears at Sonic, who leapt up and grabbed the ring.
She used a ring-powered home attack on him, knocking her to the ground.
"All right, Shadow. What's goin' on here?" Sonic said as he sat up.
"You'll find out." he said then they felt the room shake. "Sonic, your time is running out!" he said and flew through the hole in the hall.
Meanwhile Chris, Tanaka, Knuckles, Amy, and Tails entered the computer room. Eggman slammed his fist on the console.
"He tricked me! My own grandfather tricked me!" Eggman said.
Suddenly a door sealed away the Chaos Emeralds.
"The Chaos Emeralds!" Knuckles said.
Gerald's message played on the big screen.
"The countdown marking my final revenge on this world has begun! In just a few minutes, you will be destroyed. Soon, Space Colony ARK will hurtle through the atmosphere and crash into this planet with devastating force!" Gerald said.
Only twenty minutes remained. Everyone around the world saw Gerald's message.
"You have no time to prevent this disaster, and absolutely no hope of survival. Your ruler took my granddaughter Maria from me, so I'm destroying everything you care about. Now you'll feel what I felt when I lost Maria. You will see. You will see. You'll see!" he continued.
"Who is that guy? And what does he mean?" Amy asked.
"That is Professor Gerald Robotnik, He was a scientific genius and my grandfather." Eggman said.
Gerald's message repeated.
"The countdown marking my final revenge on this world has begun!" he said and the space colony shook again.
"Hey, it feels like this place is breaking apart!" Knuckles said. "This feels like an Angle Island repeat three years ago!"
"Soon it's going to get a lot worse." someone said.
Knuckles turned to see Rouge approaching.
"I've just checked the colony's propulsion systems. The computers are locked, so we can't reverse course. Looks like there's nothing we can do." she said.
"Grandpa, destroying a planet is one thing, but destroying your grandson is another." Eggman said.
Sonic stood at the entrance of the room.
"What's going on here?!" she asked.
"Sonic!" Chris said.
"If you came here for a showdown, Sonic, forget it. Soon we'll all be vaporized." Eggman said and Sonic joined the others.
"Come on. Don't be such a quitter, Eggman. Maybe if we work together, we can get out of this mess." she said. "Just like any other time like before." she whispered him.
As she looked at Gerald's message, Eggman typed on a computer.
"When I hacked into the database on Prison Island, I found my grandfather's diary." he said and handed the computer to her, and Chris looked over his shoulder and read along.
"Revenge. That is all that matters to me now." Chris read out loud.
In the flashback, the GUN soldiers were breaking into the lab.
"When I began my research, I only wanted to do good. That's why I worked to make the ultimate creature." Gerald said.
Gerald was now shown sitting alone in the lab.
"But the leaders of the project worried that I'd use it to take over the world, so they seized my lab on Space Colony ARK. Then, they took Maria from me, and my like too on a new purpose." he said.
Gerald was now shown in his Prison Island cell.
"Instead of helping people, I would get revenge on them. Night and day I've planned, so long after I am gone, my revenge will be complete." he said and wrote the numbers 00:27:53.
Back in the computer room Chris finished reading the diary entry.
"I've done it. My greatest design is now complete - the ultimate creature, Shadow. My enemies think they've defeated me, but Shadow will carry out my orders without question. Now it sleeps, but one day in the future, it will be reawakened. Shadow will bring total destruction." he said.
The clock now read 00:17:50:00. The message continues to play around the world.
"...in the coming minutes as you helplessly await your doom..." Gerald said.
In the president's limo.
"Do we have any confirmation on this?" the president asked.
"You've just received a high-priority message from the Director of the Space Agency, Mr. President. Space Colony ARK is moving toward the planet at high speed. The impact will be catastrophic, and it will cause massive destruction." Christina said.
"But if that colony hits us, millions of lives are going to be lost!"
The others looked grim.
"Good luck, Sonic. Even you're going to have trouble saving us this time." Sam said to himself.
At a building several police officers kicked down a door and aimed their weapons at several government agents inside.
"Freeze!" officers said.
"This is a warrant for your arrest. It took a long time, but the truth is out." Captain said.
Topaz and the GUN Commander watched from a rooftop.
"The secret room inside the Intelligence Agency had all records of Project Shadow. We didn't have a clue until Dr. Eggman hacked into their system and accessed the file." Commander said.
"Good thing do come from bad sometimes." Topaz said and looked up to see the red glow of the descending ARK.
In the ARK the timer neared 00:16:30:00.
"The energy from the Chaos Emeralds has transformed the Eclipse Cannon into a mega bomb. If it detonates, the blast will be more massive than a supernova!" Eggman said.
"The energy from the Chaos Emeralds is also what's pushing us toward the planet. We have to get the Emerald and deactivate them somehow." Tails said.
"Knuckles." Sonic said.
Everyone turned to Knuckles.
"What? Why me?" he asked.
"Because you can control all the Chaos Emeralds with that." Rouge said.
'I can to.' Sonic thought.
"The Master Emerald! I can use it to shut off the power." Knuckles said and stood before the others.
"There's still time to stop the space colony from crashing, but we have to hurry. We'll only reach the Chaos Emeralds if we all work together." Tails said.
"I'll lead the way. Stay on my heels and do your best to keep up the pace." Sonic said.
"Let's get to those Chaos Emeralds before it's too late." Eggman said.
Eggman, Tails, Rouge, Bocoe, and Decoe took off to find the Chaos Emeralds while Knuckles and Sonic stayed for a second.
"We're gonna pull this off. We always do from the day I met you to this very day." Knuckles said and Sonic nodded.
"I know." Sonic said and they went to look for the Emeralds.
Meanwhile.
"Remember: if we fail, then our entire planet will perish, and so will we." Eggman said.
Decoe and Bocoe were carrying the Master Emerald.
As they enter another room, laser turrets begin to fire at them. Tails flew through the lasers while Eggman and Rouge destroyed a few turrets.
Tails reached a lever and pushes it up with all his might, opening a door. Muddy water started to cascade down upon Sonic, Knuckles, Bocoe, and Decoe. Then Knuckles punched a hole in the wall to serve as an anchor while the others hold on to his other hand. The flow passes by, and the group race through the door before it closes.
At the viewport.
"I hope they make it in time." Amy said.
"I wish there was something we could do to help Sonic and the others." Chris said.
Tanaka lay his hand on Chris' shoulder.
"Sonic will get to the Chaos Emeralds in time." he said.
"Don't bet on it." someone said.
Just then Shadow entered the room.
"Shadow!" Chris said.
Shadow smirked and looked out the viewport as the station continued its descent. Chris braced himself and headed towards Shadow.
"Master Chris..." Tanaka said but Chris ignored him.
"Please, Shadow. You can help save us all." Chris said surprising everyone even Shadow. "You believe that your whole reason for being here is to get revenge. But think about it." he said and took another step forward. "When I was in danger back on Prison Island, you decided to save me." He said the put his hand on Shadow's shoulder. "Deep down, you know you were made to help others, and that's the reason you finally rescued me!"
"Hands off." Shadow said and used his inhibitor rings to shock him, blasting him onto the floor some distance away.
"No! Chris!" Amy said and started forward, but Tanaka grabbed her arm. "He needs help."
But he shook his head. Chris struggled to stand up.
"It's useless. I made a promise to Maria, and I'm keeping it." Shadow said.
Chris started toward him again.
"Shadow, getting revenge won't bring Maria back." he said.
"So what?"
"There's still time to stop this, Shadow. Please, you have to listen to me!" Chris said and started shaking Shadow. "How can you blame people alive today for something that happened fifty years ago? Can't you see it's not fair?!"
"Don't talk to me about fair! Not after what happened here!"
In a flashback Shadow and Maria were looking at Earth together.
"Maria was my only friend, but your rulers sent soldiers to take her away from me. I tried to save her, but there were too many for me to stop." Shadow narrated. "I never saw poor Maria again. Maria wasn't a threat to anyone. All she wanted was to visit your planet, but she never had the chance."
Back on the viewport Chris struggled to stand once more.
"Please listen. It's true there are some bad people in the world, but most people are good. I know that you would agree with me if you only got to know them, just like Maria wanted to. Shadow, please. Maria would want you to be friends with people." Chris said.
Shadow was surprised at how much Chris reminds him of Maria.
In another flashback Maria was dying as Shadow was trapped in a pod.
"Shadow, please promise me... that you'll help people... and be... friends with them..." Maria said.
"Maria!" Shadow said as she struggled to move.
"I'm sure you'll be very happy down there, Shadow. I only wish that I could go along with you." she said.
Then they were on Earth.
"The world looks so beautiful from up here in space. But my grandfather says the people who live there have to face many problems." she said.
Then they were under an oak tree on Earth.
"That's why you were created. To help those people and to be their friend." she said.
Back to the Viewport Chris could barely stand. He fainted, and Shadow caught him. A tear welled up in Shadow's eye. Amy noticed it.
Tanaka picked up Chris.
"He was right about Maria. She did want me to help the people of your world." Shadow said and smirked.
'And to help my mate.' he thought.
Meanwhile ten minutes remain, and Sonic, Knuckles, Bocoe, and Decoe entered a giant chamber.
"Up there!" Knuckles said.
Suddenly a giant lizard known as the Biolizard landed in front of them and roared, scaring the hench-bots.
"Calm down. I'm not gonna let that monster get a hold of the Master Emerald." he said.
Suddenly Shadow was next to Sonic.
"Leave that thing for me." he said.
"Shadow." Sonic said.
"You and the others take care of the Chaos Emeralds, and I'll distract it." he said but she hesitated.
He glanced at her, and she finally nodded. Shadow rushed forward and Spin Attacked the Biolizard, causing it to roar.
"Let's go!" Sonic said.
The four ran toward the reactor as Shadow dodged the laser beams the Biolizard fired from its mouth. Sonic and the others carried the Master Emerald to the top of the reactor.
He struck the Biolizard with multiple Chaos Spears.
"I must remember... the seven Chaos Emeralds are the servers. Our hearts intensify their power. The controller serves to unify the chaos." Knuckles said.
"You can do it, Knuckles." Sonic said and he stretched his hands toward the Master Emerald.
"Master Emerald, I need you to help me. Please stop the Chaos Emeralds!"
Meanwhile, the Biolizard materialized several energy balls around its head before sending them toward Shadow. He dodged several of them, then spun toward Biolizard, bouncing from ball to ball before landing the final hit on the prototype lifeform.
Meanwhile, the Chaos Emeralds fell to the ground, devoid of all power.
"All right!" Knuckles said.
"Good work!" Decoe said.
Suddenly the Biolizard vanished.
"It's gone."
Then Shadow teleported in front of them.
"Chaos Control!" he said.
Suddenly the entire station shook.
"What is happening?" Bocoe said.
"We are still heading toward the planet!" Decoe said.
Eggman's voice could be heard over the intercom.
"Come in, Sonic. Do you read me? That monster is still alive! It attached itself to the outside of the space colony. It's pulling us toward the planet!" he said.
Then the Biolizard reappeared outside the space station. It fused with the colony, and was reborn as the Final Lizard.
Meanwhile, Knuckles, Bocoe, and Decoe looked on as Sonic and Shadow closed their eyes and harness the Chaos Emeralds' power to achieve their super forms.
On the viewport Super Sonic appeared in the room.
"Sonic!" Amy said.
Super Sonic laid her hand on Chris, smiled, then teleported out.
Then Super Sonic and Super Shadow appeared outside, ready to take on the Final Lizard. They dodged a laser beam it fired from its mouth.
"Let's give it our best shot!" Super Shadow said.
"All right! We can go in at full speed and finish it off." Super Sonic said.
'I have plenty of practice with teamwork.' she thought as they damaged to the Final Lizard.
Meanwhile Christina Cooper was in the president's limo monitoring the situation on her laptop. Less than five minutes remaining.
"The space colony is still rushing towards us, Mr. President. We're only minutes away from impact." she said and the president covered his head.
"Hey, what's that?" Sam said.
The three left the limo and looked up to see two tiny yellow objects swarming around a red object.
"Soon the space colony won't be able to escape the planet's gravity. It'll be impossible to stop it from crashing!" Christina said.
"Come on, Sonic. You can stop it." Sam said.
"Let's hope, but I'm afraid no one can save us from disaster now." president said.
On the viewport Chris had regained consciousness, but was still being held by Tanaka.
"You have to defeat that monster, Sonic. We're all depending on you." Amy said.
"Sonic… Shadow…" Chris said.
"Topaz, you read me?" Rouge asked on the radio.
On earth.
"Yes, Rouge. What's going on there? I don't understand what Sonic's up to." Topaz said on the radio.
Scarlet reported on the situation while Mr. Stewart looked on.
"That large red object is actually Space Colony ARK glowing as it reenters the atmosphere. For fifty years, its existence was kept a secret. In the course of our investigation, we uncovered a conspiracy within our intelligence services that now threatens the survival of this planet. Our only hope lies in the bravery of two hedgehogs who are now fighting for all of us." Scarlet said.
Danny, Frances, and Helen also watched the battle while Chuck, Ella, and Cream also watched from their apartment.
"Please, Sonic..." Cream said.
"Chao chaaaaaooo!" Cheese said.
Bokkun cheered on the hedgehogs from atop the Egg Golem, which was standing on top of Eggman's base.
"Sonic, goooooooo!" he said.
Outside the space colony ARK the Final Lizard fired three lasers from its mouth at once. The two super powered hedgehogs easily avoid them, then target the giant lizard's back simultaneously. Even though the Final Lizard was beaten, the space station continued toward Earth. It started to become engulfed in flames as it entered Earth's atmosphere.
"You're stopping right here!" Super Sonic said.
They used all their might to try and push the space station back into space. Then they heard the cheers of their friends.
"You can do it, Sonic!" Tails said.
"Give it all you got, Shadow!" Eggman said.
"If you fail, the entire planet will be destroyed!" Rouge said.
"Tough it out, you guys! And you know what you've been doing for years Sonic!" Knuckles said.
"You can do it!" Amy said.
"We know you can!" Cream said.
"Sonic!" Chris said.
"Those people need you, Shadow..." Maria said.
"I am Shadow! Shadow the Hedgehog!" Shadow said and cast off his limiters, greatly intensifying his strength. "You ready?"
"You bet! Here we come!" Super Sonic said and they prepared their most powerful move.
"Chaos!"
"Control!"
In a brilliant display of light, they used Chaos Control to send the colony back into orbit but Shadow was nowhere to be seen. The timer was frozen at 00:00:50:29.
"Maria... I did it... for you..." Shadow said.
On earth confetti fell as the people celebrate.
"Wow! That's great! I'm so happy! Thank you!" a person said.
"The Space Agency just reported in. They say that the space colony have moved back into stable orbit." Christina said.
"Thank goodness." the president said.
Christina removed her glasses.
"Sonic could be charged with violating Space Agency regulations." she said.
"You know, after all that Sonic's done for the planet, I don't think the voters would like that very much. Don't you agree?" Sam said.
"...Yes, I suppose you're right." the president said.
On the viewport.
"My grandfather was truly a genius. Ever since I was a lad, he was my one true hero. I always wanted to become a great scientist like him. But he shouldn't have tried to destroy the planet. How could he do something so wrong?" Eggman said over intercom.
"I don't know, but you helped us all to save the world." Tails said.
"I'm so happy the planet was saved. Now I can conquer it and establish my Empire!"
"You still want to take over the world?" Amy said.
"Affirmative!" Decoe said.
"You're welcome to join us if you would like." Bocoe said.
"No thank you." Tails said.
Eggman laughed as he, Decoe, and Bocoe took off in a space shuttle. Sonic entered the room.
"Sonic!" Chris, Tails and Amy said.
Sonic brightened, knowing that her friend was okay. Chris walked over to him.
"Where's Shadow?" he asked.
She looked down sadly and shook her head then handed him one of Shadow's limiters.
"Y'know, maybe Professor Robotnik wanted Shadow to stop his crazy plan all along." Rouge said.
"We'll never know. But in the end, Shadow sacrificed everything to save us all." Sonic said.
Chris started to silently cry and one of his tears fell on the limiter.
"He sure did." he said and she pat him on the back thinking about the day she lost her foster parents and uncle Chuck.
"Come on, Chris. Let's head back. Space is fine, but I like my feet on the ground." she said.
'And I have an enemy to finally end after all those years.' she thought.
"The rocket's ready! It's time to go!" Tails said.
As the group left the room and the lights dim, Sonic took one last look at the room and the view of Earth.
"Sayonara, Shadow the Hedgehog..." she said.