Sonic and Tails were at Mystic Ruins walking together when they saw Knuckles, who has his back to them.
"It's Knuckles." Tails said and Knuckles smirked standing over an unconscious Eggman.
"Eggman." Sonic said.
"Hm." Knuckles said and Sonic and Tails approached.
"What'd you do to him? Have Chomps munch on him?"
"Nothing. I found him this way."
Then Tails poked Eggman with a stick to see if he was alive and was surprised when he sat up.
"Whaah! He's alive!" Tails said.
'Damn!' Sonic and Knuckles thought.
"Of course I am." Eggman said.
"What happened?" Sonic asked.
"Chaos turned against me."
"How come?"
"Because... it wants to use the power of the Chaos Emeralds all for itself." he said and Knuckles reached for his throat.
"Tell us where Chaos is or else!" Knuckles said.
"Take it easy, Knuckles!" Sonic said.
"How dare you threaten me! I'd love to teach you a lesson, but unfortunately I have to fly!" Eggman said and mysteriously rise into the air.
"He's getting away." Tails said.
It is revealed that Eggman is being airlifted by a hot-air balloon manned by Bocoe and Decoe.
"Okay, start reeling him up." Decoe said.
"The winch is jammed!" Bocoe said.
"We can pull him up ourselves."
"No way. All that weight will burn out our motors."
"Don't just leave me hanging here like a salami!" Eggman said.
"Try not to get agitated. The cable could break."
"Just enjoy the ride."
"There's not time to lose. My plans for world domination depend on Chaos. We have to track down that renegade right away!" Eggman said.
"Roger!" Decoe said and Eggman cried out as his hench-bots flew him away.
"If Robotnik was telling the truth, we have to find Chaos fast and stop it. The second it gets a hold of all seven Chaos Emeralds, it will become too powerful to defeat." Knuckles said.
"You're right." Sonic said.
Suddenly a bright light enveloped Sonic and Knuckles.
"What's goin' on here?" Sonic said.
They studied their surroundings and saw they were at a vision.
"Quiet... I've been here before. We're back in the past." Knuckles said.
They see Chief Pachacamac and his clan in front of the Master Emerald shrine. Tikal and several Chao block the way to the temple.
"Tikal, the clan needs those seven Emeralds. It is the only way to protect ourselves from our enemies." Pachacamac said.
"But taking the Emeralds isn't the way! Please stop! You'll regret it forever!" Tikal said.
"The clan has made its choice, and we'll seize the Emeralds now. Warriors, attack!" he said and they raced toward the shrine, trampling Tikal.
"Stop it!"
The seven Chaos Emeralds appeared around the Master Emeralds as the echidnas reached the top of the shrine. Chaos emerged from the Master Emerald.
"What is this thing?!" he said.
Chaos raised its hands, and the Master Emerald started to glow brightly. The echidnas were forced to shield their eyes. The Master Emerald glowed intensely, and suddenly there was a white glow that enveloped everything. When it died down, the Master Emerald's glow died down, and the shrine was on fire.
"They're gone. All of them." Knuckles said.
"Not all." Sonic said and rushed over to an unconscious Tikal. "Are you okay?" she asked and Tikal slowly sat up.
Opening her eyes, she sees the burning shrine.
"I knew this would end in disaster. Why, Father, why didn't you listen to me?" Tikal said, got up and dashed toward the shrine.
"Hey, hold on!" Sonic said and she and Knuckles followed Tikal to the top of the shrine, where she started to pray.
"You must understand. The servers are the seven chaos. Our hearts intensify their power. The controller serves to unify the chaos. The seven Chaos Emeralds take what is in our hearts and turn it into power. Hmph... But if the heart that wields the Emeralds is full of nothing but angry and fear... then that power will being pain and destruction to the world. Oh, please, you must stop Chaos!" she said and spread forth her arms as the Master Emerald glowed, thus ending the vision.
Then they were back at Mystic Ruins.
"Are you two okay?" Tails asked.
"She's gone." Knuckles said.
"Knuckles, did you understand what she meant about Chaos?" Sonic asked.
"We have to stop Chaos from getting hold of the last Emerald."
"Hey, you guys! Look!" someone said and Knuckles panicked when he saw Chris approaching him, white Chaos Emerald in hand.
Suddenly, the ground directly underneath Chris rumbled, and a huge geyser of water launches into the air.
"Chris!"
Sonic said, leapt into the geyser and took Chris' hand. "Hold tight, buddy!" she said and with his energy sapped, Chris let go of the Chaos Emerald.
"Just hang on!" Knuckles said and leapt into the air, and karate-kicks the geyser, releasing Sonic and Chris.
Sonic landed on the ground, still carrying Chris. Then the ground started cracking, swallowing the Chaos Emeralds and Knuckles' bag of Master Emerald shards. Tails flew out of the way just in time as a massive geyser of water bursts out of the ground, then fell back in.
"So Chaos has all seven Emeralds now." Knuckles said.
"I'm sorry, Knuckles. It's all my fault." Chris said.
"That creature is more powerful than all of us. It can't be stopped."
"But we have to try." Sonic said.
'Somehow.' she thought.
Nearby, a few sad Chao float down.
Meanwhile dark clouds gathered above Station Square. Everyone stopped as the ground started to rumble. Water rushed through the sewers.
Sam was giving someone a speeding ticket.
"You were doing fifty in a 35 mph zone. But since you did ask me for my autograph, I'll let you off the warning this time." he said.
Suddenly the nearby manhole exploded into the air as water gushed out like a geyser.
"Whoa! Must be a water main break!" he said.
But that wasn't the only incident. Across the entire city, manholes were launched into the air by the sheer force of water, sending people screaming and running.
"Let's get out of here!" people said.
"Weird."
Then a giant crack formed in one of the streets, and water gushed out of it. It even burst out of the tops of skyscrapers. People fled into one of the buildings.
"You'll be safe here! Hurry!" Sam said.
Suddenly a wave swept him away. One of the waves of water exploded out of one of the buildings and formed into a giant head. The creature's eyes opened, and it roared. Perfect Chaos was born.
At the White House the President, Christina, Topaz, and Rouge were watching Scarlet on TV reporting the breaking story from a helicopter.
"Station Square is flooded! We don't know the exact cause of the disaster yet, but eyewitnesses reported that something went horribly wrong in the city's water system. As you can see, there's complete devastati- Oh my.. There's something down there..." she said then saw Perfect Chaos moving through the city and started to panic. "It's appears to be some kind of monster!"
At the SSTV Newsroom. "Tell that pilot to fly closer to the monster!" the Technician said.
At the White Houe the President and Christina took frantic calls from officials as Topaz and Rouge stood by.
Rouge was starting to wonder if Sonic will be able to fight this one.
"Counter attack is impossible!" Caller 1 said.
"Our missile launcher was caught in the flooding." Caller 2 said.
"What about fighter jets? How many do we have in the area?" Christina asked.
"Throw everything we got at it. As commanding chief, I authorize you to do whatever it takes stop that thing." the president said.
In Station Square Perfect Chaos slashed a building in half with one of its tentacles.
Meanwhile Ella, Cream, and Cheese were in the living room watching the breaking story.
"Much of the city is now in ruins! The only good news is that nobody has been seriously hurt. But the monster is still attacking us!" Scarlet said.
Suddenly Cheese started freaking out.
"What are you trying to say, Cheese, huh?" she asked.
"Don't worry, that blob would hurt you." Ella said.
"Right, we're going up to the mountains where it's safe." she said but Cheese refused to calm down. Chuck entered.
"What are you waiting for? We have to get out of here fast!" he said.
"But we can't go yet because Mister Chris still hasn't come back home." Ella said.
"Where is he?!"
Meanwhile at the X-Tornado.
"We've gotta stop Chaos somehow. Faster! We don't have much time." Chris said.
"Better hang on!" Tails said.
Below them, Sonic was running toward the city.
"If I don't get to the city fast, there won't be anything left to save." he said.
At Station Square the digital billboard showed Perfect Chaos's rampage.
"The monster is downtown, leaving a wave of destruction in its wake!" Scarlet said then Perfect Chaos destroyed the billboard.
Perfect Chaos destroyed the billboard.
At Chris' school the students were being evacuated.
"Children, we're all moving up the slope there." Mr. Stewart said. "Roger, this is Chalkboard Charlie." he said on his communicator.
"We need you back here at headquarters on the double!" and agent said over the wrist communicator.
Mr. Stewart saw Danny and Frances struggling with Helen's wheelchair.
"But I can't leave my students!" he said.
"What?! This is a direct order!"
Mr. Stewart gritted his teeth in frustration, then sighed.
"I'm sorry, I didn't copy that. Can you repeat, Homeroom?"
"Sir?" Frances said.
"Are you the last ones?"
"Yeah, the others went ahead." Danny said.
"That's good. Then follow me!"
"Okay." Danny and Frances said.
Mr. Stewart grabbed Helen's chair and ran with Danny and Frances following.
At Thorndyke Mansion Entry Chuck, Ella, and Cream were ready to leave.
"I'll wait for Chris. As a former water polo champion, I can swim both of us to safety when the flood comes." Tanaka said.
Chuck picked up Cheese, who was still upset, though not as much as before.
"Alright." he said.
Cream opens the door as she, Ella, and Chuck leave the mansion. Tanaka stays to wait for Chris.
At Station Square several people pulled Sam to safety. Among them was Jerome.
"Thanks. That was close." Sam said. "Alright! Hope they send that thing down the drain!"
"Commence attack pattern bravo." Pilot 1 said.
"Copy that, Squad Leader." Pilot 2 said.
"Let's take it down!" Pilot 3 said.
The choppers open fire on Perfect Chaos, but no damage is done.
"Switch to missile fire now." a Pilot said.
Missiles were launched at Perfect Chaos, which absorbed them and breathed them back at the choppers.
"No way!"
Then Sonic arrived in town. Seeing the carnage then a picture of Mobotropolis before beating Robotnik, he gritted his teeth and sped off into the wrecked city. Meanwhile, the helicopters were destroyed by their own missiles. The citizens watch helplessly.
"Oh my gosh! The islands are okay! We need Sonic." people said.
Eggman, Decoe, and Bocoe were sitting in a giant cockpit of some sort. The lights slowly turn on.
"Systems are go." Bocoe said.
"Let's take off!" Eggman said and a large door opened, and the giant cruiser they were sitting in started to rise. "A successful evil genius always have a Plan B. That's why I have the Egg Carrier 2. Chaos better watch out. Things are about to get really chaotic. Hahaha!"
At Station Square Sonic watched Perfect Chaos' relentless rampage.
"That's it, Chaos! Your destroying days are over!" she said, took a mighty leap into the air and spun toward Perfect Chaos' head.
"Hey, look!" someone said but the water god used a tentacle to slam him back to earth.
Then Sonic ran up one of the few skyscrapers standing and flew toward Perfect Chaos. However, the monster absorbed her, spit her out, and reared up a mighty wave of water to catch her. Sonic was lucky enough to land a floating board of wood, and rode it like a surfboard.
"Oh man!" she said.
"Sonic!" someone said and she looked up to see the X-Tornado approaching her and took hold of Chris' outstretched hand. "You all right?"
"Yeah. Thanks, Chris."
"You think.. we'll win?"
"It'll turn out okay. But Chaos is more powerful then ever, so I'll need plenty of help. Can I count on ya?"
"You bet."
"Okay, then. Let's do it!" she said and Tails flew the X-Tornado into battle.
It skillfully avoided several water spears before buzzing Perfect Chaos. Suddenly, they were overshadowed by the Egg Carrier 2.
"What's this?" Sonic said.
"Back off, Sonic! Chaos double-crossed me. Now it's payback time!" Eggman said.
"Eggman! This time he's fighting on our side?"
'That's a shock. Doesn't happen that often.' she thought as the Egg Carrier 2 closed in on Perfect Chaos.
On the Egg Carrier 2.
"All attack systems are online." Decoe said.
"Blast charges are loaded and ready to fire on your command." Bocoe said.
"You're through, Chaos! The price of disloyalty to the Eggman Empire is annihilation. Front missiles, fire." Eggman said.
At Station Square the Egg Carrier 2 fired many missiles at Perfect Chaos, but they were quickly deflected by a force field. Then the water god fired a giant laser from its mouth, destroying the Egg Carrier 2. The villains escape in the Eggmobile.
"Oh no!" Decoe and Bocke said and Sonic saw this.
"Oh, great! How are we gonna beat it now?" she said.
'I knew it wasn't gonna work?' she thought and shook her head.
Then, a bright light moved in, blinding the X-Tornado's occupants. The light surrounds the X-Tornado and safely guides it to a landing position on a bridge. Sonic leaps down from the X-Tornado.
"This just keeps getting freakier and freakier..." she said and the female echidna appeared. "You again!" she said and the light faded.
"Since the day of my father's invasion, I've jorneyed across the seas of eternal time with Chaos to help keep its power under control. But some friend woke Chaos for a plan to use its power for an evil purpose." Tikal said.
"Eggman... He must have uncovered the way to revive Chaos somehow so he could use it to take over the world."
A few flashbacks of Eggman and Chaos were shown.
Then Perfect Chaos spit out the Chaos Emeralds and the purple Emerald landed in front of Tikal. It is petrified and she picked it up.
"Chaos has now drained all the Emeralds of their power." she said.
"What?"
"Ever since my clan attacked the temple, Chaos has known only hate and anger. He will use the power of the seven Emeralds to destroy this world. We have to seal Chaos back in the Master Emerald before it's too late!"
"It won't work." Sonic said and Tikal stood up. "If we seal it in the Master Emerald, the same thing will only happen again. We have to solve this problem once and for all."
"Yes... but how can we?" Tikal said but Sonic didn't know how to answer.
"Sonic! Sonic!" someone said and Sonic looked up to Cream carrying a petrified yellow Chaos Emerald. "Look, I have something for you!" she said and Ella, Tanaka, and Chuck also arrive.
"Cream got the Emerald back after Chaos let them all go." Chuck saiddd.
Then Amy ran in carrying a petrified blue Emerald.
"Hey, Sonic!" she said.
Then Big also arrived and held up the green Emerald.
"I finally got back the pretty rock that Froggy swallowed. You can borow it if you want to." he said.
Then Eggman, Decoe, Bocoe, and Knuckles arrived, followed by Tails.
"Sonic! If you collect all the Emeralds, you can defeat Chaos!" Tails said.
Then Knuckles held out the red Emerald.
"Here. You have more experience at being a hero." he said. "Besides, you beat plenty of people. You got this."
"Thanks, Knuckles." Sonic said smiling and Knuckles turned to Eggman, knowing he hiding an Emerald.
"Robuttnik." he said and realized what he sid while Sonic froze for a second.
'Crap.' he thought and saw Tails looking at them.
"Oh, all right. Take it." Eggman said and handed over the petrified cyan Emerald.
"We need one more." Tails said.
"Sonic! Look what I found!" someone said.
Chris was coming with the last Emerald: the white one but tripped and fell on his face so Sonic ran over.
"Chris!" she said and he looked up.
"Sonic, look!" he said and held out his Emerald.
"I knew you'd come through."
The crowds cheer for Sonic from the wrecked buildings.
"Go, Sonic! Yeah, Sonic! All right!" the crowd said.
Then the Chaos Emeralds' power started returning.
"The Emeralds are getting their power back!" Chris said and the Chaos Emeralds started levitating and started to orbit Sonic.
Sonic closed her eyes and let them change her into Super Sonic. Her quills stood up, and she rised into the air.
"I thought that the power of the Chaos Emeralds could only be awakened by hate and anger." Tikal said.
"There are other feelings that are even more powerful." Knuckles said.
"When everybody gave their Chaos Emeralds to Sonic, it was because of our friendship. Caring is stronger than hate, and that's how Sonic is gonna beat Chaos." Tails said.
Then Sonic finished changing into Super Sonic and turned to Perfect Chaos, who prepared itself for battle. Perfect Chaos projected a barrier around itself, but it was smashed by Super Sonic. Then Perfect Chaos turned its tentacles into drills, but she spun into them, shattering them. Not even Perfect Chaos' laser mouth can hurt her, so it fired an even stronger laser that headed toward Chris and the others. Super Sonic moved in front of it.
"Aaahhh! ... Sonic!" Chris said but the beam did nothing.
"You can't stop me!" Super Sonic said.
'Especially after that experiment I got done.' she thought as the others smiled.
Mr. Stewart and his class cheer her on from a hill far away from the city.
"If anybody can stop that monster, Sonic can." Helen said.
"Go, Sonic!" Danny said.
The kids cheer with chants of "Go, Sonic!" Perfect Chaos whipped a tentacle toward Super Sonic, but she used a hand to stop it, and then used Chaos energy to dissolve it.
"Is that the best you can do?" she asked.
Perfect Chaos fired a laser beam from its mouth again, but she charged headfirst toward it, and forced it back to sender. Once she flew inside Perfect Chaos, he exit again as the water god glowed gold and vanished in a bright light. The crowds cheer. Super Sonic had won. However, the puddle that was Chaos landed on the ground, and it revert to its base form.
"It wasn't destroyed. It survived!" Knuckles said.
'God this reminds me of the Dingo fight!' he thought.
"Chao chao chao." Cheese said.
Then many other Chao rise from the water and surround Chaos, including Cheese. Chaos beamed.
"But it doesn't look angry anymore."
"Yeah. If you ask me, Chaos actually looks kinda happy." Tails said.
"Wow, look at all those Chao!" Cream said.
"I wonder where they came from?" Chris said.
"It looks to me like those Chao were friends of Chaos who came here to see him." Amy said and Tikal stepped in front of Chaos.
"These are the Chao you kept watch over." Tikal said and Chaos looked around at the Chao and there was a flashback of Chris, his friends, and the Chao. "They are coming into this world now. The Chao will live here in peace, and you can be at peace now too." she said and the flashback ended. "Time to go." she said, spread forth her hands, and she and Chaos rise into the air.
They soon vanish and Sonic looked at the city in concern. Then Tails broke the silence.
"Huh? Where'd Eggman go?" he said.
"I think he escaped while we were distracted." Tanaka said.
"Yeah, well, he won't get away next time." Knuckles said.
Then Chris approached Sonic.
"You did it, Sonic!" he said and Sonic turned around.
"We all did." she said and he returned the thumbs-up.
Meanwhile, Big is underneath the bridge, fishing.
Later Sonic, Tails and Knuckles were at Tails' Workshop.
"Alright spill. Why did Knuckles call Eggman Robuttnik?" Tails asked with his arms crossed.
Sonic and Knuckles looked at each other.
"He has to know. He's our best friend and I said Robuttnik by accident." Knuckles said and Sonic sighed.
"My mom is Queen Aleena. I left to stop Eggman once known as Robotnik." she said and Tails looked at her in shock.
"OK then. Why didn't you tell me?" Tails asked then looked at Knuckles. "And how long have you known?"
"I found out a while ago. I actually worked with her, Sonia and Manic." Knuckles said and Sonic snickered.
"Yeah, and started dating Sonia." Sonic said smirking and he glared at her.
Then he shoved her but she still smirked.
"We didn't tell you because Sonic didn't want any attention." Knuckles said and Tails nodded.
"Please don't tell anyone. I'm not ready." Sonic said and he nodded again.
"OK." he said.