Shadow was at Prison Island thinking in his cell. Security official Howard Watcher narrated as several shots of the island were shown, showcasing the various security gadgets.
"Shadow's in the underwater isolation cell. It's impossible to escape from there, and even if he could, where's he gonna go once he breaks out? Prison Island is surrounded by the sea. There's no land for miles, and everybody knows Shadow ain't no swimmer. We got guards keepin' lookout in the towers twenty-four hours a day, and the laser alarms will go off the second they detect the slightest movement. The entire prison is wired with surveillance cameras, metal detectors, and sound monitors. Not even a fly could escape from here! This place was built to hold the toughest crooks in the world, but in all the years that Prison Island's been in business, there hasn't been one single solitary breakout! Hope Shadow likes it here, 'cause he ain't leavin'!" Howard said and laughed then pointed to the image of Shadow on the screen. "Don't think of pullin' any funny stuff while I'm on duty, 'cause I got my eye on you, Shadow!" he said and laughed again.
"I'm sure Shadow is innocent and something is wrong with Sonic, but there's nothing I can do to help them." Security guard said to himself.
In Shadow's cell Shadow was trying to figure out what happened.
On Tanaka's boat.
"We are still quite far from Prison Island, but we can't take this motorboat any closer because of their radar. Their security systems are so advanced that they would spot us long before we reach the coast, and if they do detect us, they well send out armed boats to intercept and arrest us." Tanaka said.
"So, what are we gonna do?" Chris asked.
"Luckily, I've thought of a way to thwart their system. It is high-tech, so we will fool it using my low-tech solution." he said as his glasses shone.
Then the boat deployed a swan boat.
"They'll be looking for motorboats, so this paddle boat will let us duck under their radar." he said.
"Hm..." Chris said and they board the swan boat and started pedaling. "I don't know about this, Mr. Tanaka. I feel kinda goofy."
"We can make it. We just have to paddle faster." he said and they pedaled faster toward Prison Island.
Inside Prison Island two security guards detected the swan boat moving erratically toward them.
"Sir, somebody is heading toward the island." Security Guard 1 said.
"Really?" Security Guard 2 said.
"It looks like a giant... duck, sir."
"That's no bird. It's a boat. Somebody's trying to sneak onto the island. They think they've fooled us, but I'll make sure they're sunk before they reach land."
"Do you really think a paddle boat poses that much of a threat?"
"Who knows? It's better to destroy 'em first and ask questions later."
Outside Eggman arrived in his Eggmobile laughing.
Then he pressed a button disrupting the TV screens' signals, turning them to static.
"What? Whoa, what? Sound the alarm! We can't, sir. The system's going haywire! Call the cell blocks! They're jamming our communications! It's an attack!" Security Guards said.
Eggman laughed a victory laugh.
In Eggman's base.
"He did it! He's back on Prison Island!" Decoe said.
"Dr. Eggman rules!" Bocoe said.
"All right!" they said together and high fived.
In the forest Eggman was hovering idle with his hands clasped behind his head.
"I wonder if I'm pushing my luck, breaking into the place a second time." he said then communicator screen activated.
"Perhaps. The security on the island has been upgraded since your last visit. You must be careful. When they restore communications, they will send robots to stop your team." Decoe said.
"Their robotic designs are greatly improved. With their new defenses, it will be almost impossible to enter that compound again." Bocoe said.
"Well, nothing is going to stop me from breaking in and taking those Chaos Emeralds. Sonic said I need to obtain all seven Emeralds in order the Eclipse Cannon." Eggman said.
"But are you sure it's worth the risk, Doctor?" Decoe asked and Eggman grinned.
"Once I get that cannon working, I'll be unstoppable!" he said to himself.
Then Rouge and Sonic arrived.
"Okay, Eggy, fill me in." Rouge said.
"According to Rouge, the Chaos Emeralds are stored in a vault inside the compound. I must have them."
"No prob. Just leave it to me."
"Do not trust her!" Decoe said.
"She wants it for herself!" Bocoe said.
Eggman shut off the screen.
"They get on my nerves. Let's get down to the nitty-gritty, shall we? In the first phase of my plan, I'll go around the island wreaking havoc and drawing the guards from their posts, clearing the way for you two to enter the compound. Then, Sonic moves in. She'll blow up the whole island by sneaking into the weapons center and setting off all the ammunition stored there with this miniature detonation device." he said and tossed a time bomb to Sonic, who nodded. "Meanwhile, Rouge will proceed to the warehouse where the Chaos Emeralds are locked away and remove them. We will then meet up at the rendezvous point and make our escape. We have exactly thirty minutes. If you run into trouble, you're on your own."
Then Sonic and Rouge nodded.
"Let's go!" Sonic said and they left.
Soon Eggman fired several missiles at the facility. Various GUN robots emerged to attack Eggman, but he nimbly dodged their attacks and fired back in return.
"Peekaboo!" he said.
Meanwhile the X-Tornado flew into the vicinity.
"What's going on?" Amy asked.
"It looks like somebody's fighting." Tails said.
"We'd better get down there and find Shadow and Sonic!"
The X-Tornado landed near Rouge and Sonic, and Amy threw herself at Sonic, thinking she was still on their side.
"Oh, Sonic! What a relief! I came here to rescue you, but you escaped all by yourself and look like you're on our side again! ... Sonic?" she said then her mistake, and also seeing a smirking Rouge nearby, cried out and let go of Sonic. "You're not the Sonic I know like before! What are you doing here?"
Then the Eggmobile hovered in front of her.
"None of your business. Now get lost." Eggman said.
"Dr. Eggman!" she said
Tails was surprised to.
"Sonic, Rouge, carry out your assignments!" Eggman said and blew a hole in the door with a missile, and Rouge and Sonic entered the facility.
Then he bearded down on Amy, who took a few stepped back.
"I'll take care of you..." he said.
"Keep away!" she said.
"Amy!" Tails said and quickly converted the X-Cyclone to the X-Tornado and chased Eggman into the sky. "I can't rescue Shadow or Sonic 'til I get Dr. Eggman out of the way."
"This will send Tails into a tailspin!" Eggman said and fired lasers and rockets at him, but he dodged them.
Then he found himself at the front of the X-Tornado, trying to keep one step ahead of the craft.
On the ground, Amy recalled Sonic.
"I wonder what she's doing here?" she said to herself and entered the facility. "Don't worry, Sonic! Shadow! I'll find you and help Sonic!"
Inside an alarm sounded as Sonic searched for the ammunition warehouse.
"Sonic will speed through the building and sabotage the weapons center."
Elsewhere, Rouge flew around searching for Chaos Emeralds, even nimbly crossing a laser field.
"Meanwhile, Rouge will sneak into the warehouse. Once she gets in, she will grab the Chaos Emeralds."
She found the red Chaos Emerald.
"I can feel those Emeralds here. All I have to do is break into the vault and help myself." she said and found the keypad. "Ah. Cracking the code will be a cinch."
After pressing a few buttons on the keypad, the door opened, granting her access to the Chaos Emerald.
Outside Tanaka and Chris were scaling the steep cliff. Suddenly there was an explosion above them as Tails and Eggman exchanged fire.
"Take this! ... He'll see. Tails can't outfox me!" Eggman said then his communicator screen activated.
"Hey, Dr. Eggman! Forget him! You have more important things to do!" Decoe said.
"Stay focused!" Bocoe said.
"I'll have to crush Tails another day." Eggman said and stopped in front of Tails, forcing him to stop in midair. "Now look, Tails. Just because I'm leaving doesn't mean you win. This only a time out, you hear me?! A time out!" he said and flew away.
Tails blinked in surprise before landing in his original position in front of the hole the missile explosion made. Then he opened the cockpit and looked around.
"Amy! ... Where'd she go?" he said.
Eggman had never really left, as he flew back onto the island.
"I have to see what Sonic and Rouge are up to." he said.
Meanwhile, Chris was scaling the cliff alone. A flashback of last night came to him.
"Don't worry. I'll be out before you know it." Shadow said.
"Shadow..." he said.
'Sonic, what happened to you?' he thought.
Inside Prison Island Rouge had collected both the red and cyan Chaos Emeralds, and Sonic had installed the time bomb, labeled Eggman Bombom.
"Doctor, the detonator is ready to go, but I need to know how long to set the timer for." she said on the radio.
"Good work, Sonic. You can set the detonator to go off at exactly fifteen minutes. Will that be enough time for you, Rouge?" Eggman said over the radio.
"I can be out of here in five minutes easy." Rouge said over the radio.
"All right, then. Set the detonator for ten minutes."
"Right, Doctor." Sonic said over the radio then set the bomb for ten minutes and left.
Meanwhile Shadow was in his cell then looked up to see Amy in the distance. A tube extended from the facility to his cell, bring her with it. Soon she was right outside his cell.
"Bet you're surprised to see me! I rushed here to rescue you from this awful island then get Sonic back to normal. You ready?" she said.
Inside Prison Island.
"Intruder alert! Intruder alert!" Intercom said the facility went on lockdown, shutting all its doors. "Gold Beetle, go bonk those bozos!" he said and new-and-improved GUN Beetles teleported away. "Flying Dog, sniff 'em out!"
The robot called Flying Dog moved out.
Howard snickered.
"Flying Dog is the ultimate security robot, specially designed to fetch any trespasser. Flying Dog will keep hounding its prey until it's cornered, and then it pounces, decimating its foe with rabid ferocity!" he said.
"Not every trespasser is dangerous, you know." Security Guard said.
"My motto is "Take no prisoners; we have too many inmates here already." Howard said and laughed.
Back in Shadow's cell Amy drew her Piko Piko Hammer.
"I'll open your cell now. You'd better stand back, Shadow; I wouldn't want you to get injured." she said.
"I don't know, Rose. These bars are pretty strong." Shadow said.
"Well, I happen to be pretty and strong too."
Then a Gold Beetle materialized behind Amy.
"Rose! Look out!" Shadow said.
Amy turned around and hammered the robot to pieces.
"Don't you know it's rude to show up someplace uninvited?! And don't bother me when I'm trying to rescue Shadow!" she said.
"Nice."
"Now I'm gonna bash down the bars of your cell, Shadow."
"No, Rose!"
"Don't worry, Shadow. My feelings for Sonic will give me the strength to free you and find her."
"I let them drag me to Prison Island on purpose so that I could learn what happened to Sonic."
"Huh?" she said.
"Did you see her? Do you know where she is now?"
"When Tails and I landed here, we saw Sonic near the entrance being ordered around by Eggman."
He crossed his arms.
"I should have known that Eggman would be involved in this mess." he said.
Amy noticed the markings in the wall.
"Have you been doing math on your wall?" she asked.
"That was there before. Watch out!" he said and broke out of the cell. "I need you hammer your way out of this prison." he said.
"Let's go!" she said.
Inside three hits was all it took for Amy to bring down the door.
Howard had detected the breakout.
"Shadow's out!" he said.
Then an alarm went through the base.
Outside Chris, was still on the cliff and heard the alarm.
"Now what?" he said but remembered something Tanaka told him earlier.
"It is too dangerous. You stay here and I will find Shadow and maybe Sonic." Tanaka said.
"Sorry, Mr. Tanaka. I can't stay behind if Shadow and Sonic's in danger." he said and kept scaling the cliff.
'Even if it's Sonic doing this.' he thought.
Meanwhile, Shadow carried Amy outside through the hole, where they met Tanaka and Tails.
Tanaka bowed.
"I'm relieved to see you're safe, Shadow, and Mr. Chris will be too. Shall we go?" he said.
"Hi Tanaka! Long time no see! How's everything going with Chris?" Amy said.
"Can't we catch up on how are friends are doing later, Amy?" Tails asked.
"He's right. Now get moving. I still have to track Sonic down." Shadow said and leapt out of sight.
Inside Rouge had uncovered a third Chaos Emerald, the purple one.
"Lovely..." she said.
Suddenly the Flying Dog appeared in the doorway.
"Hello there. I hope you didn't come to get my Emeralds back."
"Intruder located. Security units proceed to level 5. Prepare to attack." Flying dog pilot said as she started to flee. "Hold it."
She dodged the lasers the Flying Dog fired, then avoided its missile and rebounded off a wall destroying one of its missile launchers.
The time bomb was at 5:13 and counting.
Outside Shadow saw Sonic fleeing in the forest below, and landed in front of him.
"Sonic, this is it. I want answers. What are you up to?" he asked. "You're not yourself!"
Sonic smirked.
"You'll find out."
They clashed several times. Shadow even manages to land a hit on Sonic.
Inside Rouge finally destroyed the Flying Dog, but the door closed, preventing her from escaping.
"And just when things were going so well..." she said.
The time bomb was now at three minutes and counting.
"Red alert! An explosive device has been detected in the security area! Begin emergency evacuation immediately!" Intercom said.
Outside Tanaka was at the bottom of the cliff near the swan boat, but Chris was nowhere to be seen.
"Mister Chris! Where are you?" he said and returned to the top of the cliff. "He's gone! He must be on the island somewhere!" he said surprising Amy and Tails. "I must go and find Mr. Chris fast! Mr. Chris!" he said and they followed him.
In the forest Shadow and Sonic were still fighting. Then Sonic's wrist communicator activated.
"Come in, Sonic. Sonic, do you read me? I have a little problem on my hand." Rouge said over the radio.
Inside Rouge was slumped against the door.
"I'm sort of locked inside the vault with the Chaos Emeralds. There's no way to open it from in here, so I'm stuck." she said on the radio.
"I can't talk. I have to go now!" Sonic said over the radio.
"You mean... you won't help me?"
The sound of Sonic's fighting came from the other end of the radio.
"Not right at this second, no." she said on the radio.
"You can't leave me. Remember, I have the Emeralds."
Back in the forest.
"I'm busy right now!" Sonic said on the radio and bashed by Shadow and returned the blow.
Inside.
"I should have known not to count on that shady character for any help!" Rouge said and tried to break down the door, but to no avail.
In the forest as the Prison Island staff evacuated, Chris ran through the forest searching for Shadow and Sonic.
"Shadow... Sonic..." he said.
Inside Rouge sighed.
"I'm finished, and worse than that, I'm losing three Emeralds, too..." she said.
In the forest.
"Sonic, come in now! Sonic!" Eggman said on the radio.
But Shadow and Sonic were still fighting. Then Sonic's wrist communicator activated.
"Sonic, where are you? The detonator will go off any second! You have to get off the island now or you're going to be blown sky-high! Do you read me?" Eggman said over the radio.
"Oh no!" Shadow said.
"I'm not waiting for you and Rouge any longer. You two are on your own." Eggman said over the radio.
"I have to get everybody off the island!" Shadow said and was about to flee.
Sonic watched Eggman fly over the clearing. Just then Chris saw Sonic, and thought he was Shadow.
"I found him! It's Shadow!" Chris said but stopped. "That's not Shadow..." he said to himself. "Sonic?" he said but got no answer.
Sonic saw a vision of Maria.
"Maria..." she said to herself.
'I'm sorry Chris, I'll explain one day.' she thought.
Inside.
"When I found three Emeralds, I thought this was my lucky day..." Rouge said.
"Rouge, this is Sonic. Come in." Sonic said over the radio.
"I'm here." she said on the radio.
"Do you still have the Chaos Emeralds?"
"Of course I still have them."
"I'll be right there to pick them up."
"She's coming for the Chaos Emeralds, but what about me?"
In the forest Chris was shocked at what Sonic said next.
"Dr. Eggman, I'm going back in to pick up the Chaos Emeralds for you." Sonic said on the radio.
Chris stood there in shock.
Only one minute remained until the bomb explodes.
"Sonic, promise me..." Maria said in his head.
"Yes, Maria. You will be avenged!" she said to herself. "Chaos Control!" she said out loud.
Chris ran toward her.
"Sonic! She's the one they want! Now I can prove Shadow's innocent!" he said to himself. "As much as I don't want her in trouble."
Then Tanaka arrived.
"Chris, waaiit!" he said.
Chris grabbed Sonic the moment she used Chaos Control, causing both of them to disappear.
"Chris?" he said and fell to his knees. "He is gone..."
As he started to break down, Shadow grabbed him and carried him to safety.
Inside Sonic and Chris appeared inside the vault.
"Sonic!" Rouge said as Sonic shoved Chris aside and took the Chaos Emeralds from Rouge. "Oh, what the...?"
Only ten seconds remained until the bomb explodes.
"Let's go!" Sonic said.
"Hey, hold it, Sonic. You're not gonna leave this kid behind."
"It doesn't matter to me what happens to that boy anymore."
"Hold on! Our friend got arrested 'cause of you. He's still here. We have to get him off the island. ... Please, will you help me? I have to rescue Shadow somehow? He would rescue you if it was the other way around. You have to help him please!"
In Sonic's mind, the image of Chris changed to Maria.
"Please, Sonic..." she said in her head.
"Maria..." Sonic said to herself and used Chaos Control seconds before the island exploded in a violent fiery eruption, taking Rouge and Chris with her.
The explosion even reared up a small tsunami. It was now dusk, and Eggman watched from a distance before he flew away. The X-Tornado escaped safely.
"Mister Chris... Oh... Mister Chris!" Tanaka said.
