Knuckles and Tikal ran as fast as they could through the base when they heard the alert about the self-destruction of the base. It had taken them 10 minutes while walking so they couldn't afford to slow down. Knuckles was much faster than Tikal so he ended up carrying her by piggyback, otherwise she wouldn't make it out alive. Because of the self-destruct, all the machines in the base had shut down, making it an easy run to the dock area. Once they were there, they met up with Sonic, Tails and Amy, who were waiting by the sub. Without any explanations, the crew leapt into the Tsunami and Tails drove it out of the base, and just in time, because as soon as the Tsunami was out, the base exploded. The explosion would create another tidal wave that would strike the mainland but the Tsunami was unaffected. Everyone sat down in relief when they were clear of the base, but Sonic was clearly disturbed about something. He was showing a look of anger and depression. Seeing this expression, Tikal grew a little nervous, as it telegraphed that something bad had happened.
"Did you guys find the Master Emerald fragments?" Tails asked.
"We've got them. We're fine now." Knuckles replied.
"Sonic, are you ok?" Tikal asked.
"Huh? Yeah, I'm fine." Sonic replied.
"Fine? Eggman got away with the chaos emeralds!" Amy exclaimed.
"What?" Knuckles asked.
"I said Eggman got away with the Chaos Emeralds."
"How could you let him get away with the Emeralds?"
"Because we were too late." Tails replied.
"What actually happened?" Tikal asked.
Flashback
Sonic, Tails and Amy had found their way into a very tall circular room. The walls were painted red and grey, with Eggman's logo painted everywhere. There was a large circular dish in the centre of the floor. It had a line straight down the middle, where it looked like it would split in half and open. Amy had her hammer in her hand, ready for anything. Sonic was also preparing for anything that could happen. Tails was looking around the room. By the design, he could tell that it was a launching tube of some sort. This meant that Eggman could launch something from this tube at any time.
"Ok Eggman, come out wherever you are." Sonic called out.
"Sonic, we need to find the control room. That's where he would be." Tails said.
"But where could it be?" Amy asked.
"Knowing a base like this, I'd say the top of the base."
"But what is this room?"
"I think it's some kind of area where Eggman could launch some missiles or weapons of some sort."
"Then perhaps we should destroy it." Sonic suggested.
"I cannot allow you to do that." A booming voice bellowed. The floor then opened and a huge, mechanical human-like machine emerged. It was designed to look like Eggman, even complete with the moustache. It looked like a machine that he had made before, when Sonic had battled him on the Death Egg several years ago, except that it was much bigger. Sonic, Tails and Amy were looking at the machine with a look of horror. Sonic was reminded of the machine he destroyed on the Death Egg. Eggman's voice was then heard from the machine.
"Well, well, well. You found a way to get to me did you?" Eggman asked evilly.
"Ok Eggman, time to be cracked!" Sonic scolded.
"I wouldn't try it. All 7 chaos emeralds power this machine. You cannot destroy it, even if you tried."
"You're powering that with the chaos emeralds?" Tails asked.
"Exactly! Now I can create the Eggman Empire easily. Sadly, you will not be around to witness my triumph." With that, rocket launchers from the feet of the machine and it blasted away from the platform. When the roof opened, water began flooding in, forcing Sonic, Tails and Amy to run from the room. When they were out, Sonic turned to the closed door and began cursing.
"Eggman, I'll get you for this!" Sonic shouted.
"What do we do now?" Amy asked. Before anyone could answer, there was a voice coming from the bases' computer.
"Warning! Warning! Self-destruct sequence activated. Base will self-destruct in T minus 5 minutes."
"Eggman's activated the Self-destruct!" Tails exclaimed.
"We've got to get out of here!" Amy added.
"Hold on!" Sonic shouted. He grabbed Tails and Amy's arms and ran as fast as he could towards the Tsunami.
End Flashback"Eggman's using the power of the chaos emeralds again?" Knuckles asked.
""Yes. I don't think there's anything we can do." Tails replied.
"Not true. Now that we can complete the Master Emerald, we can stop him." Tikal said.
"Of course, the Master Emerald can drain the power from the Chaos Emeralds." Knuckles added.
"But what will we do then?" Amy asked.
"The emeralds will only be deactivated for a brief moment. As soon as they've been deactivated, someone will need to get inside the machine and steal them."
"You can do that easily." Sonic said.
"But who will use the Master Emerald to deactivate the Chaos Emeralds?" Tails asked.
"I will." Tikal replied.
"You can do that?" Amy asked.
"I've used it before."
"Then what?" Tails asked.
"If Knuckles can get the Emeralds to me, I can use them against Eggman." Sonic replied.
"Sonic, no!" Amy moaned.
"It's our only option."
"Oh, ok." Amy didn't like it when Sonic turned into Super Sonic, but there were times that he may have to.
"Ok, now we need to get to Angel Island." Knuckles said.
"I'm on it." Tails replied.
After a few minutes, the Tsunami arrived at the Angel Island, which had been unaffected by the tidal wave caused by the explosion of the base. Tails was able to convert the Tsunami into a semi-glider so it could land on the Island. When they landed on the island, everyone quickly climbed out of the Tsunami. Knuckles and Tikal immediately ran over to the Master Emerald with the last few fragments. The fragments were placed near the Master Emerald. The emerald glowed and attracted the fragments. The Master Emerald had now been fully restored. Reacting to the Master Emerald's power, Angel Island began to levitate once more. Knuckles and Tikal both smiled with satisfaction, even thought hey knew it wasn't over. They still had to track down Eggman and recover the Chaos Emeralds.
"Ok, the Island has been restored." Knuckles said.
"We still need to track down Eggman." Sonic added.
"No need guys, look!" Amy exclaimed. Eggman had found them. The machine he had left him was rapidly approaching the Island. It landed on the island and Eggman's voice was heard from the machine.
"So, you survived that explosion." Eggman scolded.
"Wasn't hard." Sonic scoffed.
"Of well, looks like I'll have to kill you all now." The fist of the machine came smashing down towards the Island. Sonic was only just able to evade it. He began running around the island at top speed to keep Eggman's attention away from Tikal, who was at the Master Emerald.
"Sonic, I will kill you now!" Eggman scolded. He had no idea of what Tikal was doing at the Master Emerald. He continually tried to hit Sonic, but was having no success. Knuckles had climbed on one of the pillars around the altar, ready to jump towards the machine once the Emeralds were deactivated. Tikal was now invoking the Master Emerald's power.
"The servers are the 7 chaos. Chaos is power…enriched by the heart. The controller is the one that unifies the chaos!" As soon as Tikal finished the line, the Master Emerald began spinning rapidly. It was only then when Eggman realised what Tikal was doing.
"Stop!" Eggman shouted. He prepared to fire a Chaos laser at the Master Emerald, but he wasn't quick enough.
"Please, stop the Chaos Emeralds!" Tikal shouted. The Master Emerald glowed green and released a flash of white light. At that moment, the Chaos Emerald's lost their power and Eggman's machine deactivated.
"Knuckles now!" Tails shouted. Knuckles leapt at the centre of the machine and broke his way inside. Within a few seconds, he had retrieved the Chaos Emeralds and emerged from the machine.
"It's over Eggman." Knuckles gloated.
"Not quite, you annoying pigs. The machine still has some of the Emeralds power." Eggman replied. The machine started up again and reactivated. It was running on power that had been copied from the Chaos Emeralds. The machine was just as powerful but now unable to fire the Chaos laser.
"Sonic, you're up!" Knuckles shouted. He threw the chaos emeralds at Sonic. He immediately caught them and invoked their power. There was a flash of yellow light that blinded everyone briefly. When they regained their sight, they saw that sonic had transformed into Super Sonic. Rather than fleeing, Eggman became even more determined.
"Ok super-freak. You may be super strong now, but I still have another trick of my sleeve." Eggman gloated. One of the machine's arms reached out and touched the Master Emerald. Rather than destroying the emerald, some power was absorbed, supercharging the machine.
"No, what have you done?" Knuckles asked.
"I just burrowed a little power from the Master Emerald. Now I shall destroy you all!"
"I'd like to see you try." Super Sonic gloated.
Eggman fired a Chaos laser right at Super Sonic. Sonic was able to block the attack without any damage. He then flew at top speed towards Eggman and tried to pummel him. The machine was able to block every single blow that Super Sonic threw. Super Sonic was on the offensive and forcing the machine backwards. Eggman chuckled and the machine began flying. Eggman tried to smash Super Sonic from behind, a blow that Super Sonic evaded easily. Eggman was on the attack this time. However, every blow that he launched was either blocked or evaded. Eggman also tried firing chaos lasers, but these were easily blocked. What Eggman didn't realise was that every time the chaos laser hit Super Sonic, he gained strength rather than got wounded. As a result, Super Sonic was getting even more powerful. Super Sonic realised this but was holding back, ready to unleash a surge of power at a critical point. Back on the Island, Tails, Amy, Knuckles and Tikal were watching the battle from a safe distance. Amy was incredibly worried about how Super Sonic would fair. Nobody could tell that Super Sonic had the advantage.
"I hope Sonic's wining." Amy said.
"I'm sure he's fine. We'll just have to wait." Tails replied.
"Is there anyway we could help?" Tikal asked.
"No Tikal, it's up to Sonic now." Knuckles replied. They continued to watch the battle between Eggman and Super Sonic. Eggman had fired a few more chaos lasers, not realising that this was only making Super Sonic stronger.
"Are you ready to give up hedgehog?" Eggman asked.
"Not yet, I'm just getting started." Super Sonic replied. It was at that moment when Super Sonic unleashed the power that he had built up. Super Sonic suddenly went on the offensive, throwing blasts that Eggman couldn't block at all. Every blow that Super sonic landed caused severe damage to the machine. Eggman was eventually forced to eject from the machine and take off in his egg mobile. The main machine was quickly destroyed by Super Sonic's power. Super Sonic then returned to Angel Island and reverted to his normal form. Knuckles had returned the Chaos Emeralds to their places around the Master Emerald. Eggman was completely flabergastered as to how he had been defeated.
"But how? The Master Emerald powered that machine. How could I lose?" Eggman asked in frustration.
"Easy, every time you fired that chaos ray, it made me stronger." Sonic replied. Eggman was stumped at that revelation.
"Curse you Sonic! I will have my revenge." Eggman shouted. He powered up the egg mobile and, as usual, got away, leaving Sonic, Tails, Amy, Knuckles and Tikal on Angel Island.