While Knuckles and Shadow were gone getting the emerald, Cosmo and Cream helped Tails make last minute adjustments and check-ups to the Typhoon. It had been some time since they had used the Blue Typhoon for anything serious, probably not since they were out in space.
By the time Shadow and Knuckles had arrived back with the Master Emerald, the Typhoon was ready to go. Tails allowed his two sidekicks to assist him in installing it and within the hour they were ready to go. After Tails had finished analyzing everything, he told Sonic that he couldn't be 100% sure it would overpower Eggman's Chaos-Creation, but it had a fighting chance.
'Are we ready?' Cream asked glee fully as she sat in her usual seat of the Typhoon.
'Let's go!' Everyone exclaimed.
Tails gracefully brought the Typhoon into the air and off they went. The Typhoon was sufficiently larger than the Tornado, allowing everyone to travel on board. Knuckles remained in the control room with The Master Emerald, trying to prepare it for the battle ahead, while everyone else remained in the base or headquarters of the ship. Usually Sonic and Amy would be the co-pilots for Tails, but this time rouge had to take over for Amy. Sonic couldn't deny it not feeling the same, as much as he liked Rouge and all.
'Don't worry, Ames, I'm coming for you.' Sonic said out loud to himself.
After Tails had tracked down the base again, he put the ship into stealth mode, allowing the ship to be so quiet you could hear a pin drop. He hovered above Eggman's base and allowed Sonic, Shadow and Rouge to drop to the ground. Cream and Cosmo geared up in some smaller ships, charged with the Master Emerald's power, ready to attack as soon as Eggman put up a fight. Tails and Knuckles stayed on board to keep the ship steady and to control the Master Emerald. The more the plan unraveled, the more confident they all felt it would work. Honestly, they have the emerald that is more powerful than anything else, what could possibly go wrong?
'Gah! That pesky Sonic is back!' Eggman exclaimed as he saw the three drop to the ground through his cameras.
'Don't worry, Doctor, they can't over power your machine.' Decoe assured him.
'That is right, it is far too grand!' Bocoe added.
'He has a plan, I'm sure of it. He won't give up!' Amy shouted from her cage in the corner of the room.
'As much as I hate to admit it, the brat is right. Sonic is a pain but he isn't that stupid. I'm sure he has something up his sleeve.' Eggman said as he stroked his moustache.
'What should we do, Doctor?' Bocoe questioned, almost in a panic.
Eggman continued to stroke his moustache as he thought about Bocoe's question. He hummed to himself as he thought about a plan, a plan brewing in his ingenious, evil mind. When he had it, his eyebrows rised, showing his eyes were widening behind his dark glasses. An evil smile grew across his face as he turned his head to face Amy. Amy grew increasingly nervous as she watched him look at her, knowing she would be a part of his plan.
'Sonic will fight me, no hesitation. Even if he doesn't have a chance, he'll give it a shot.' Eggman thought allowed.
'What are you saying, Doctor Eggman?' Decoe asked.
'Maybe Sonic needs a new opponent. Someone a little more difficult for him to take on.' Eggman chuckled as he continued to stare at Amy.
'Oh no…' She whispered.
Sonic, Shadow and Rouge hid behind a few trees, watching the entrance to the base. Nothing. Tails and Knuckles watched on from the Typhoon. Nothing. Cream and Cosmo watched on from their separate ships. Nothing. Where was he? Where was Amy? This all seemed too easy.
'What do you make of it?' Rouge asked.
'He knows we're here. He's waiting for us to make the first move.' Shadow replied.
'What do you think, Tails?' Sonic asked through his wrist communicator.
'Nothing is going to happen until we do something. I say Rouge goes forth and cracks the code to the entrance, when you're in you go and find Amy. Call us again if you need back-up.' He replied.
'Copy. Alright, Rouge, you're up.' Sonic said as he nodded to Rouge.
Rouge nodded back before flying over a few bushes and landing gracefully back on the ground. She walked toward the door, where a small keypad was attached to the side. She inspected it for no more than thirty seconds before she realized what the code was. She cautiously keyed in a few digits and letters before it lit up green and the doors began to open.
Still nothing. Suspicious…
Rouge turned around and gestured for Sonic and Shadow to come out and follow her.
'Nice work.' Sonic gave her the thumbs up.
'Not really, that's child's play for this one.' Shadow jumped in.
'I'm going to take that as a compliment.' Rouge smirked.
Sonic and Shadow rolled their eyes before the three walked through the doors to the base. They walked a few steps in before they could see a small, petite figure in the distance. A small, petite, pink figure, sitting gracefully on a small seat in the middle of the next room, her back facing them.
'AMY!' Sonic shouted before he prepared to bolt towards her.
'No, Sonic!' Shadow shouted as he grabbed the blue hedgehog's arm.
'Shadow! What are you doing?!' Sonic exclaimed, trying to free himself.
'Don't you think that's awful suspicious, Sonic?' Rouge asked him. 'Call out to her again, see if she answers.'
'Amy? Amy, answer me!' Sonic yelled.
It appeared as though she heard him this time. Her head rose, still facing away from them. Sonic took a few steps towards where she was sitting, calling her name again. She turned her head, so she was only just looking over her shoulder at them. Her shoulder and entire side of her face looked bruised and swollen.
'Sonic?' She whispered.
'Amy! I'm here.' Sonic said with a smile as he was about to run towards her.
'Stop.' She said calmly as she put a hand up, forcing him to stop. It was as though she had released some power from her hand that pushed him away from her.
'Please, Amy. We are here to take you home!' Rouge exclaimed.
'You have to go. Leave me, save yourselves. I'm begging you.' Amy cried.
'Never.' Sonic said, almost in anger as he got away from Shadow and Rouge and ran towards the pink hedgehog.
She stood up, turned around and pushed him away, causing him to fall backwards and land on his behind. Amy let more tears slide down her cheek before she bowed her head in shame. Suddenly, the Chaos-Creation 6000 appeared as if from thin air behind Amy. Now Sonic and the others understood, a luminous pink ray of light was connecting Amy to the beast, controlling her every move.
'Tails? You may want to prepare yourself.' Rouge said over her own communicator.
'What are you talking about? Did you find Amy?' Tails asked.
'Well, yeah.' Rouge admitted.
Suddenly Amy raised her arms and threw them forward, causing Sonic, Rouge and Shadow to be thrown all the way out the front door of the base. The metallic beast forced Amy to walk forward and follow them outside. They got to their feet and watched on as Amy and the machine came out of the front entrance. Cream and Cosmo flew down and hovered by Sonic and Shadow's sides.
'OH HOHOHO! Hello there!' Eggman exclaimed as he appeared behind the beast in his small hovercraft and flew down to hover beside Amy.
'Eggman, you've gone too far this time! Let Amy go!' Sonic exclaimed.
'Oh, I really don't think so. You certainly won't be getting her back anytime soon!'
'Wanna bet?' Sonic said with a cocky grin, making Amy nervous.
Eggman grew angry at Sonic's confidence. He looked at Amy who was standing with weak posture, the machine was draining her energy. He commanded the machine to make her walk forward, as weak as she was, she could still intimidate her loved ones.
'Come on, Ames. Snap out of it!' Sonic exclaimed.
'I… can't.' She whispered.
'Knuckles! I think we might need some help around about now!' Cosmo exclaimed over her ship's communicator.
'Got it, Cosmo!' Knuckles replied to her before raising his arms up towards the emerald. 'Oh, Master Emerald, hear our plea! Lend us your mighty power for good! We wish to overcome the powers of evil! Evil is using your follower's power! Save the chaos emeralds, help us set them free!'
The large, green emerald began to glow uncontrollably before it shot out rays of light all around the Typhoon. It sent its power to Cream and Cosmo's ships and to Sonic and Shadow, turning them super. Eggman began to sweat and panic as he watched his enemies become more and more powerful.
'How?!' He exclaimed.
'The Master Emerald. It will overcome all the other emeralds.' Amy said more to herself than anyone else.
'Not if I can help it!' Eggman shouted before he smacked his hand down on a large red button.
Amy let out a painful screech before the luminous, pink ray lifted her up into the air. She called out for her hero to help her but it was no use. Electrical currents were circuiting through her at an alarming rate before suddenly they stopped. Mid-air, Amy's body went limp.
'Amy?!' Cream and Cosmo exclaimed in sync.
Amy reacted to their call and raised her head. She opened her eyes and stared deep into their souls. These were not Amy's eyes however, they were dark and evil. Completely black except for fluorescent red pupils. Tails and Knuckles watched on from above in complete horror, knowing what Eggman was doing to her.
'Sonic! Eggman is using the emeralds at their full capacity! You have to destroy the machine!' Tails exclaimed.
'But be careful, if you hit Amy even in the slightest she will…' Knuckles trailed off, sending pain through the rest of the gang's stomachs.
'We're on it!' Sonic exclaimed confidently before he leapt towards the machine.
Before Sonic could even get close to the machine, Amy shot forward and let out a screech as she pinned him down to the ground. Sonic held her hands in the attempt to keep her away from him, but she fought hard to get her hands around his neck.
'OH HOHOHOHO! This machine is even better when it's set to mind control!' Eggman cackled.
'Well, that explains a lot.' Tails said to himself.
'Sonic! It's not Amy doing it, it's Eggman!' Knuckles exclaimed over his communicator.
'I've figured that much out, Knux! Rouge and Shadow! Help me distract Amy! Cosmo and Cream! You need to destroy the machine!' Sonic exclaimed, still trying to fend Amy off.
Shadow and Rouge ran towards their infected friend, ripping her away from the blue hedgehog. This made her angry, really angry. She let out a scream before taking on Rouge in a battle, which Rouge was easily able to defend. Rouge was able to force herself to throw in a few punches or kicks here and there, distracting Amy long enough for the other two to join in and finish it.
Rouge tackled Amy to the ground by her waist and barely held her down. She almost escaped until Shadow stepped in and trod on her arms. It appeared as though the possessed Amy feared the power of Super Shadow.
'Sonic! You have to knock her out!' Rouge exclaimed as she held Amy down.
'No way! I'm not going to hit her!'
'For Christ's sake, Faker! We need to knock her out so we can destroy that machine easily!' Shadow exclaimed.
Cream and Cosmo still tried to shoot at the metallic beast but it wasn't working. Even with the power of the Master Emerald their guns were of no use. One of Cream's guns broke down, leaving Cosmo to battle it nearly alone.
'Guys! You have to help us, now!' Cream shouted, holding back her fearful tears.
'I can't hurt her, Shadow!' Sonic repeated.
'Fine then, I will!' Shadow exclaimed over all the noise.
'What?!' Eggman exclaimed when he heard this.
Eggman tried to fly forward and stop the hedgehog from stopping Amy but he was too slow. Cream and Cosmo flew in and kept him away. They aimed their guns towards him, sending him into a state of panic, suddenly realizing they all had him surrounded. They were going to defeat him again.
'Decoe, Bocoe! Retreat!' Eggman exclaimed before flying away, his two sidebots running after him.
Shadow took in a deep breath before closing his eyes and using his super powers to knock Amy hard enough to put her lights out. The pink ray behind her suddenly faded away, making her body go limp. Sonic felt as though his heart had just been torn in two, watching her be so brutally hurt. Rouge flew up into the machine which now began to malfunction and stole away every last chaos emerald.
'We have to go, now! It's going to explode!' Rouge exclaimed.
'I swear to God, Shadow, if you've hurt her-'
'I did what I had to do!' He shot back.
Sonic picked an unconscious Amy up bridal style and jumped onto the wing of Cream's plane. Shadow and Rouge jumped onto the wings of Cosmo's plane before they quickly got themselves back up to the Blue Typhoon. Seconds later, the Chaos-Creation 6000 exploded into millions of pieces, taking Eggman's base with it. Two birds, one stone really.
The team watched on as flaming debris floated and fell back down to the ground before they finally took off and headed back towards home. They finally had Amy rose back with them, safe.