In Metropolis, Eggman was determined to make the Sonic Team pay for Metal Sonic's destruction. But after some modifications and implanting a Chaos Emerald, Metal Sonic was now Metal Sonic 3.0. He was a mainly black robot with the same cosmetic features.

"At last, my Metal Sonic 3.0 is complete!" Eggman exclaimed as Metal approached him.

"Now Metal Sonic, go to Tails' workshop and destroy!" Eggman commanded.

"Affirmative," Metal Sonic said as it flew out of the base to the workshop.

At Tails' workshop, Tails and Cream were talking, Prof. Samuel went back to Neo Green Hill, and Knuckles and Simon were talking as well.

"So, who exactly are you?" Knuckles asked.

"I'm Simon the Echidna," he replied, "You may be the last echidna on Mobius, but on my planet, there are many echidnas."

"Hmm, interesting," Knuckles said, "Planet Neon, was it?" Simon nodded his head.

"How come I've never heard of it?" Knuckles asked.

"The planet appears every ten years," Simon replied, "My friends and I have been here for that amount of time."

"Do you plan to go home after this?" Knuckles asked.

"At first, I really wanted to go back, but I've gotten used to Mobius," Simon replied, "So have my friends."

"You and your friends go way back, right?" Knuckles asked.

"Yeah, ever since we were kids," Simon replied, "basically, I'm responsible for them since I'm the oldest." Suddenly, a laser blast came out of nowhere and was in close range of the workshop.

"What was that?!" Cream asked worriedly.

"Chao!" Cheese said in fright.

"Tails, you and Cream find a safe place!" Knuckles commanded.

"Okay!" Tails said as he and Cream left for a safe place. Knuckles and Simon came outside to see Metal Sonic, only different.

"Metal Sonic?!" Knuckles exclaimed.

"3.0!" a voice said.

"Eggman!" Knuckles exclaimed.

"Yes," he said, speaking from Metal Sonic, "Metal Sonic has received an upgrade, and a deadly one at that!"

"Hmph! No matter how you change something, it's the same thing," Simon explained.

"You haven't seen the power Metal Sonic possesses! Attack 3.0!" Eggman demanded.

"Simon, Metal Sonic can copy our abilities, so watch your back," Knuckles explained.

"Gotcha!" Simon understood as they prepared to battle.

Sonic, Rouge, and Amy went to Central City to find Shadow. They decided to split up in order to find him. Sonic went off by his own while Rouge and Amy went together. They communicated through communicators that Rouge had.

Sonic was running around the city for 5 minutes until he saw a familiar black hedgehog on a rooftop. Sonic pressed a button on his communicator.

"Rouge, Amy, I've found Shadow," Sonic said.

"Got it, Sonic. We're following your coordinates now," Rouge said.

"And don't do anything stupid!" Amy shouted.

"Yeah, I'll try to reason with him," Sonic said. He ended his communication and went between two buildings. Sonic did a wall jump between them until he got up to the roof. Sonic approached Shadow cautiously.

"Hello, Shadow," Sonic said. Shadow turned around to see the blue hedgehog smirking.

"What do you want, Sonic?" Shadow asked, hating to be bothered by Sonic.

"Long story short, we need your Chaos Emerald," Sonic explained. Shadow huffed.

"Hmph, like I'll give you my emerald," Shadow said.

"Shadow, the planet is in danger," Sonic said, "just give me your emerald."

"Like hell I will!" Shadow said, getting more frustrated.

"Shadow," a voice said. Two figures arrived on the roof and turned out to be Rouge and Amy.

"Rouge," Shadow said. Rouge then approached Shadow at a slow pace.

"Shadow, Sonic is right," Rouge began, "we need your Chaos Emerald. We'll return it after all this."

"C'mon, Shadow. What would Maria say?" Sonic asked. Shadow then thought about these words until he came to an conclusion.

"Very well. I'll give you the emerald," Shadow said.

"Sweet. Thanks Shadow," Sonic said.

"But I get the emerald as soon as this is over," Shadow said, "And no funny business."

"Yeah, all right," Sonic agreed, "Let's get back to Tails' workshop." Sonic, Rouge, and Amy started to leave but noticed Shadow was still standing.

"Shadow, you coming?" Amy asked.

"You just asked me to give you my Chaos Emerald," Shadow replied, "Nothing more. I'm not coming."

"We could use your help Shadow," Rouge said.

"Hmph, I'm sure the 'fastest thing alive' can handle it," Shadow retorted.

"Okay, Shadow. Be like that," Sonic said, "You know where to find us."

"Whatever," Shadow said as he sped his way away from Sonic.

"Come on, let's go," Sonic said. The three of them left to regroup at Tails' workshop.

Back in Green Hill, the battle started out as a few punches and kicks but soon became more heated.

"Hmm, you may have an upgrade, but I can still defeat you!" Knuckles exclaimed as he ran up to Metal Sonic to attempt to give an uppercut but was blocked.

"What?!" Knuckles asked shocked.

"Rejected," Metal Sonic said as he threw Knuckles a few feet.

"Let me try distracting him," Simon said, "Yo Metal!" Metal turned his sights to Simon.

"Unknown lifeform, must destroy threat," Metal Sonic said.

"Catch me if you can," Simon said as he ran around at a normal pace, gaining Metal's attention. Metal tried to fire lasers at Simon but fails.

"Now's my chance," Knuckles thought. Knuckles then pulled out two silver hand sized metal shovel gloves made to accustom his namesakes.

"Shovel Claw!" Knuckles exclaimed as he dug through the grass and into the ground, following the land's seismic waves to get under Metal Sonic. Eventually, he was directly under Metal, who was still being distracted by Simon.

"Now, Knuckles!" Simon exclaimed. Immediately, Knuckles burst through the ground, catapulting Metal in the air.

"My turn!" Simon said as he jumped into the air and knocked Metal to the ground with a kick. Metal landed on the ground hard with some damage on cue with Simon.

"Knuckles, distract him," Simon said.

"Got it!" Knuckles agreed as he started to brawl with Metal. Simon was gathering energy to perform his attack.

"Knuckles, move!" Simon exclaimed. Knuckles moved out of the way.

"Mind Wipe!" Simon exclaimed as a burst of white energy surrounded Metal, causing it to stop moving because of his temporary scrambled programs.

"Knuckles, finish him while he's confused," Simon ordered.

"Got it!" Knuckles exclaimed, "Quake Punch!" He then gathered all his strength to emit a power a shockwave powerful enough to catapult Metal Sonic back to Metropolis. Simon ran up to Knuckles.

"Nice moves, Knuckles," Simon commented.

"You too, Simon," Knuckles said. Tails, Cream, and Cheese then came from their hiding place and approached the echidnas.

"Is Metal gone?" Cream asked.

"Long gone," Knuckles said.

"Boy, you guys must've had your hands full," a voice called out.

"Sonic?" Tails said.

"The one and only," Sonic said as he, Amy, and Rouge approached everyone.

"What happened here?" Amy asked.

"Metal Sonic got an upgrade," Knuckles said, "but it wasn't much smarter."

"Yeah!" Simon exclaimed. Suddenly, something caught his eye.

"Hey, what's that over there?" he asked as he pointed at a purple object near the battle area.

"Could it be?" Rouge asked.

"The final Chaos Emerald!" Sonic exclaimed as he ran up and picked up the emerald.

"Now we have all the emeralds, right?" Tails asked.

"Yep. We got Shadow's emerald," Sonic said as he pulled out the Green Chaos Emerald.

"Hooray!" Cream exclaimed.

"Chao!" Cheese said.

"Okay, so now what?" Rouge asked.

"We contact the others and get this over with," Sonic said.

"I'll call Maroon and the others," Simon said.

"I'll get Silver and Blaze. They should be in Green Hill," Tails said.

"And I'll call the Chaotix," Sonic said.

"And I'll contact the Professor," Rouge said.

"What about Shadow?" Knuckles asked.

"I don't think he wants anything more to do with this," Amy said.

"Okay! We got the plan, now let's call!" Sonic exclaimed.