It's another typical early afternoon in the city of Station Square. Potted flowers bloom, Flickies sing, adults are at their jobs, and it's just about the end of the school day. Oh, and Dr. Eggman once again flies over the city with another new plan for world domination. The doctor's newest model Egg Carrier casts its shadow over the city as the familiar X-Tornado flies towards it from the side, carrying Sonic (who is wing-riding), Tails, and Amy.
Scenes like this have become fairly normal for the people of Earth ever since Sonic charged into Dr. Eggman's base back on planet Mobius to stop him from using the power of the Chaos Emeralds for his energy amplifier. An accident occurred during their battle, and an uncontrolled Chaos Control blast sent Sonic, his friends, Dr. Eggman, his robotic assistants, and the Chaos Emeralds across dimensions until they wound up on planet Earth. With help from new friends like Christopher Thorndyke, his family, his butler and maid, and the military, Sonic and friends have continued their battle against Dr. Eggman to protect the people of Earth.
Having spotted the X-Tornado, Dr. Eggman puts his plan to steal the Master Emerald from Angel Island on hold to shoot his enemies out of the sky. All the cannons open fire on the aircraft, covering the sky with explosions, but Tails' flying skills are just too good, as they escape the aerial inferno without a scratch. Knowing that the people will be in danger if they fight above the city, Tails launches several missiles and Vulcan Cannon shots to get Eggman to follow them out to sea, like when they fought against the original Egg Fort.
Eggman quickly caught on to what Tails was attempting to do and said, "Decoe! Bocoe! Get the Egg Carrier back to my island fortress! I'll resume my dastardly plan once my Egg Wyvern blows that scrap heap out of the sky!" So saying, he climbed into his Eggmobile and took off for the hanger underneath the main deck. Sitting in the hanger was the Egg Wyvern, a massive robot resembling the creature of the same name. The robot is mostly red, with some spots of silver, black, and white as well. After his Eggmobile is attached to the top of the robot's head, Eggman initiated the launch sequence, and soon it shot out of its hanger, heading for the X-Tornado at a high speed!
Back on the Egg Carrier's bridge, as they turned the ship around to return to the island, Decoe and Bocoe started a conversation. "How badly do you think the boss is going to lose to Sonic this time?" Decoe asked. Bocoe replied, "I am sure that it would not be any worse than that time that creepy Sonic robot showed up." Suddenly, Dr. Eggman's messenger, Bokkun, piped up, "Who cares? As long as he's away, his stash of candy and ice cream is left unguarded!" Decoe and Bocoe panicked at this and, after setting the autopilot, chased after Bokkun to prevent him from going on a sugar rush.
Meanwhile, back above the Emerald Coast, Sonic has just caught sight of the Egg Wyvern and calls, "Heads up, Tails! Eggman's launching a new weapon at us! Do a barrel roll!" After checking the position of Eggman's attack, Tails sent the X-Tornado spinning, just narrowly missing the Egg Wyvern's rush!
After the X-Tornado came out of its spin and the Egg Wyvern slowed down enough for Eggman to turn around to face the X-Tornado, he called through the loudspeaker, "Impressive reflexes, fox boy! But my Egg Wyvern is more than a match for your puny X-Tornado!" He then began to charge up the Egg Wyvern's lasers, aiming them all for the X-Tornado and firing once the lock-on was confirmed. Before the attack could hit, Tails pulled a lever and shouted, "X-Tornado, switch to Battle Armor Mode!" The plane suddenly moved extremely quickly, causing the lasers to hit the water below, and transformed into a two armed ship! As Sonic and Tails prepared to battle, Amy opened the cockpit and summoned her Piko Piko Hammer as she climbed out and prepared for battle as well.
Eggman covered the cockpit with a protective canopy, then made the Egg Wyvern do an aerial flip before firing several electric projectiles out of the tail at the X-Tornado, only to be knocked down when Tails brought up the shield on the right arm. He then flew closer and brought out the blade on the left arm in an attempt to destroy the Egg Wyvern right away, but Eggman swooped out of the way and, after the X-Tornado stopped in midair, began to fly circles around it while everyone watched to see what Eggman would do. After flying around a few times, Eggman stopped and, after doing another flip, called, "Here I come!" He then broke into a glide as he went flying towards the X-Tornado!
Amy shouted, "He's going to ram into us!" Sonic ran onto one of the wings and called, "I've got an idea, Tails! On my signal, get beneath Eggman!" Once the Egg Wyvern was close enough, Sonic called, "Now!" and leapt off the wing towards Eggman while Tails and Amy got out of the way. Sonic grabbed onto the horn of the Egg Wyvern, holding on tight to avoid getting knocked off. As Eggman struggled to shake Sonic off, Tails got close with the X-Tornado once again, allowing Amy to leap towards the robot with her hammer ready. Once she was on top, she brought it down and shattered the canopy while Sonic grabbed her and got them both back onto the X-Tornado. "N-no! Not the canopy!" Eggman cried. "Hey Eggman, what's the matter?" Sonic called. Eggman growled back, "You! I'm not finished yet!"
Eggman quickly fired off the lasers again, one managing to hit the X-Tornado and causing it to shake and spark a bit in the air. In response, Tails fired the Vulcan Cannon at the Egg Wyvern, managing to hit several critical points on it in spite of the plane shaking. Taking this opportunity, Amy summoned her hammer once again and threw it at Eggman's robot, causing the Egg Wyvern to start spewing smoke! "This is it, Eggman! Prepare for another defeat!" Tails called. "Guh! I won't go down like this!" Eggman shouted.
While Tails held the X-Tornado stationary so it could stop shaking, Eggman once again began to circle it. "Tails, you'd better move! Eggman's up to something!" Amy called. Tails responded, "I can't yet, Amy! We could have a burn-out if we try to move now!" With his circling completed, Eggman went in for the victory, only to have Sonic break into a Spin Attack and go rushing towards him as he came in. Sonic's attack hit the control unit for the Egg Wyvern, causing it to fly off-course and miss the X-Tornado, Sonic hanging onto the robot to avoid falling into the water below. Before it exploded, Sonic revved up and made a leap when the robot was angled up towards the shore, using it as a makeshift ramp to jump for the beach!
As the Egg Wyvern exploded, the blast increased the distance of Sonic's jump, not only allowing him to land on the Emerald Coast beach, but also in a palm tree for a soft landing. As he looked back up, he saw Eggman escaping in his Eggmobile back to his island fortress.
After Sonic got down from the tree, Tails called down to him, "Way to go, Sonic! Want a lift back home?" Sonic called back up to him, "That's alright, Tails! I'm gonna go for a run, so I'll see you back at Chris' house in a little while!" Amy called down, "Be back soon! I'll bake you a nice surprise for your victory!" With that, she climbed back in the cockpit as the X-Tornado switched back to its regular form. Although it was still a bit damaged, it quickly took off back towards the Thorndyke mansion as Sonic took off running across the beach.
After running along the beach for a while, Sonic arrived at Emerald Town. He always enjoyed visiting the little beach town due to its laid-back atmosphere. It was built months ago by the government after Eggman had established a casino area called Night Babylon in an attempt to turn the people of Station Square into gambling addicts so he could earn more money for his doomsday machines. The plot was eventually stopped by Sonic, Tails, Rouge, and Chris, and afterwards, the government had it torn down and had a new town built in its place. Since then, the surrounding area had gotten back to its former green glory from before Eggman had built the casino.
Finding a relaxing spot under a palm tree on the beach, Sonic got comfortable and lazily watched the clouds drift by. Even he had to admit that the beach was a nice spot to relax, as long as it didn't involve going near the water. He began to drift off into a nap when a sound snapped him out of it.
Jumping to his feet, Sonic looked up at where the sound was coming from to see a military helicopter, seeming to be headed in the direction of Station Square. Wondering if something was going on, Sonic decided to head back to Chris' house and find out if anything had happened. Deciding to get some fun in on the way, he opted not to take the highway and instead headed through the Neo Green Hill Zone that was Emerald Town's most famous landmark, dashing over the checkerboard-patterned hills and through the corkscrews that reminded him of the Green Hill and Emerald Hill Zones back on Mobius as he headed for Station Square.
Meanwhile, at Dr. Eggman's island fortress
As the Eggmobile finally arrived at his island fortress, Eggman noted with some satisfaction that the Egg Carrier seemed to be back in its underground hanger. After that loss to Sonic, he was in no mood to go after the Master Emerald. Landing the Eggmobile on its landing pad, Eggman headed for his room, seeing Decoe and Bocoe struggling to keep Bokkun pinned to the ground as he walked.
"C'mon! I want my ice cream!!" Bokkun cried. "Your ice cream? It belongs to Dr. Eggman!" Decoe replied. "What was that?!" Eggman yelled. All three robots jumped to attention, Bocoe replying, "Oh, Dr. Eggman! After you left, Bokkun tried to raid your storage for sweets! We were trying to keep him from going crazy again!" Eggman glared at Bokkun and yelled, "How many times do I have to tell you?! Stay out of my Nutball Crunch Ice Cream!!" While Bokkun started bawling, Eggman went to the kitchen to fetch his "World's Best Boss" mug, filling it with hot water. As he grabbed a teabag, Bocoe asked, "What about your plan to steal the Master Emerald, doctor?" Dipping the teabag in the water, Eggman replied, "My Egg Wyvern was no good. I must come up with another strategic strategy and dastardly design before I go after the Master Emerald." Before going into his room, he said, "Make sure my El Gran Gordo case is spotless! And afterwards, I don't want to have to deal with any of your snooping as usual!"
Going inside and locking the door, Eggman set the mug down on the coffee table and sprawled out on his bed, grinning as he looked at the pictures of Ella, the housemaid for the Thorndykes, on the wall at the end of his bed, beginning to relax.
At the Thorndyke mansion
After running through the Neo Green Hill Zone, Sonic had been on the outskirts of the city, making it a short trip afterwards to reach the Thorndyke mansion. As he approached the gates, they opened to let him in and Mr. Tanaka opened the front doors of the mansion, greeting him as he slowed down.
Walking into the living room, Sonic was greeted by all of his friends. Tails, Amy, Cream the Rabbit and her Chao friend Cheese, her mother Vanilla, Chris, his grandfather Chuck, and the housemaid Ella. Amy revealed that she had baked Sonic a pie, and Tails added that it was a good thing Sonic had gotten back so soon or else he would've eaten it. This earned a laugh from everyone. Afterwards, they prepared to enjoy a snack and hear about what went on earlier when the sound of helicopter blades caught everyone's attention.
Everyone headed for the back door, since it seemed like the helicopter was landing on the landing pad in back. As they opened the door and stepped out, everyone was surprised. It was the military helicopter Sonic had seen earlier, and stepping out of the door on the side were Topaz, Rouge the Bat, and Shadow the Hedgehog, all top-ranking agents for G.U.N.'s military branch.
Sonic spoke first, "Shadow, what's going on?" The black hedgehog replied, "We are here to request your help, Sonic. It's a direct order from the president and Commander Tower."