I believe that Sonic CD takes place before Sonic 2. There's quite a bit of evidence to suggest it if you add all SEGA games into SegaSonic. I wonder if you've noticed the other Sonic universe lines yet.
All copyright info on first chapter
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Sonic Adventure Zero – Death of Angels
By Master hunter
Chapter 5 – A Super Discovery
Sonic reached a corridor with huge windows looking out into space. He felt his heart pound faster and he began to sweat much more the usual. It was like reaching the heart of Scrap Brain; no matter how cool you were you were still nervous when you reached the end.
The corridor led to a giant room. Another screen appeared with Eggman's face on it. The sounds of jets broke the deafening silence as a Robot Sonic appeared from the highest part of the room. It landed softly on the floor and looked up to Sonic.
"This is it? The big fight? Another Robot Sonic! This one looks even worse than the last one", said Sonic laughing.
"No this isn't the big fight. This is just a warm up", said Eggman.
"I am Mecha Sonic. Priority one, destroy Sonic the Hedgehog. Initiating attack modes", said the Robot Sonic.
Mecha Sonic span into a ball and quickly spin dashed towards Sonic. It was easy enough to jump over. Although as Sonic landed on the floor he was hit in the back by the machines ram mode. Sonic fell to the ground and jumped straight back up again as he began to hit the Robot with his own spin attack. As he hit the machine he noticed the metal spikes oscillating like a saw. Sonic quickly decided to stay away from them. A couple of hits later Mecha Sonic span into a ball again, only this time he jumped into Sonic and Sonic jumped expecting another Spin dash. Sonic fell back to the ground into the opposite direction to Mecha Sonic.
"You're pretty tough after all. Not bad, but I'm better", said Sonic.
Mecha Sonic tried to ram Sonic again. This time though Sonic got a few more hits on the machine and it started to spark. It went into a ball and jumped across the room again, firing spikes in down towards Sonic. Sonic back flipped to avoid them and made a desperate dash towards Mecha Sonic. He managed to get the final hit he needed to destroy the machine.
As it exploded a door at the opposite side of the room opened up. Behind it was Eggman at another computer console, hitting it hard with his fist in a moment of pure frustration. He looked up to find Sonic smiling at him. Eggman panicked and ran as fast as he could away from Sonic. Sonic laughed as he slowly ran to chase Eggman. Sonic could've easily caught Eggman but decided to have some fun instead. This ended up being a mistake as Eggman jumped into a dome shaped like the evil villains head.
Sonic skidded to a halt as a huge machine appeared in front of him. The machine's size was only eclipsed by the huge arena Eggman had built especially for this fight. The machine was 5 times as big as Sonic. Sonic swallowed a very big gulp as in front of him was the real fight, the ultimate battle armour, The Egg Robot.
"Now Sonic. This is the real fight", said Eggman.
"Bring it on Eggman", said Sonic.
The Egg Robot started to walk forward. Sonic didn't take any time to think as he made a spin jump directly at the machine. Sonic used all his strength to avoid the spikes he was going to hit if he kept attacking like he did. Deviously Eggman had placed spikes on the end of the Robots arms, at the exact height Sonic jumped at. Sonic ran to the other side of the room and watched the Egg Robot carefully.
Every time he takes a step forward one of the arms moves back while the other arm moves forward. I got it!
Sonic made a well timed jump that landed a hit precisely when both arms were at the same point. He waited for the next opportunity but the next time Eggman took a step back and Sonic just crashed into the floor. The Egg Robot then flew into the air.
"Amazing, that huge thing can fly?" asked Sonic in amazement.
Sonic dashed around the arena as Eggman tried to crush him. Eventually the Egg Robot crashed back to the floor. This time Sonic found himself facing the machines back. Eggman laughed as several bombs were fired out of his back, each one shaped to look like Eggman. Sonic dashed between the Robots legs as the bombs exploded. He looked back to find one of the spiked arms had been fired at him like a missile. Sonic came within an inch to the opposite wall as he skidded to stop himself crashing into the wall. He expected the spiked arm to hit him but found that the arm had returned to its original position and the other arm had been fired. The other arm reached a point before returning to its original position.
Eggman laughed as the machine flew back into the air. This time Sonic stood still and waited for Eggman to drop. He made sure this time the machine's back was next to a wall. It started walking again, which allowed Sonic to make some well timed jumps again. Several hits later and The Egg Robot started to spark a little.
"All that, and he's only sparking a little. This is some armour", said Sonic.
The Egg Robot ascended into the air again. Sonic waited for the drop and just narrowly avoided each spiked arm as it was fired. He needed all his focus on dodging the attacks so he couldn't get any of his attacks in. The machines flew into the air and crashed into the ground, it started to walk again. Sonic smiled as he got some good hits in this time and the Egg Robot was sparking like crazy.
"NO! THIS ISN'T HAPPENING", shouted Eggman.
Sonic made one last hit and the Egg Robot started to explode. The Chaos Emerald that had powered it fell to the ground and Sonic quickly grabbed it. Sonic ran far enough away from the explosion, which opened up a pathway out of the arena into Space. However the explosion also affected the Death Egg's computer and it was about to explode, sending the huge space station crashing back to Earth.
Sonic wasn't going to wait to see what happened. He'd rather die in peaceful space than blow up inside the Death Egg. He ran into space and prayed that somehow everything would work out fine. Then the Chaos Emeralds started to glow.
Meanwhile, back on Earth an explosion could be seen in the sky. Tails became overcome with worry as the explosion only got brighter. No doubt Sonic had won but how was he going to get back to Earth. A flicky flew to Tails and handed him a note.
Something has fallen from space into the sky. It looked like a golden flame but I can't be sure. It could be your friend. I've calculated where it's likely to land and if it is him he's going to need your help. Fly into the skies above the ocean to the west and you should see him.
MP
Tails jumped into the Tornado and noticed a fleet of flickies were following him. He took off towards the place the note told him to go.
Sonic sighed as he watched the Death Egg crash back towards Earth. He could do nothing but watch it all and die peacefully when the artificial atmosphere created by the Death Egg disappears.
So this is how it ends. Earth looks so peaceful, I'm glad I could save it one last time…I won't let him die like this…huh? I can feel a warm energy surround my body.
Sonic opened his eyes and found himself surrounded by a golden aura. His usual blue fur had been replaced by golden fur. He stood in space, breathing normally, with his spikes pointing up and his eyes turning red (though he hadn't noticed those things yet). He had completely transformed and felt stronger and faster.
"Way past cool", said Sonic, "Is this the power of the Emeralds?"
It was then that he realised it must have been as the emeralds had disappeared. He then realised it might not be permanent and headed back to Earth. He broke into Earth's atmosphere and found that the friction fire from re-entry wasn't hurting him. He was invincible.
He looked down and saw Tails in the Tornado, searching frantically for him. Sonic then rejoined his new sidekick and flew around the Tornado. Tails looked shocked.
"Sonic is that you?" asked Tails.
"Yep, cool isn't it?" asked Sonic.
"But how?" asked Tails.
"The Seven Chaos Emeralds must have done this to me", said Sonic.
"So you don't need my help after all?" asked Tails.
Sonic started feeling a little weaker so stood on the wings of the plane. He reverted back to his blue self and saw the Chaos emeralds move away from him. Not wanting that power to disappear he quickly grabbed all the emeralds again by unexpectedly jumping towards them. Tails had to have amazingly fast reflexes and an amazing flying ability to make sure Sonic didn't fall to his death. Luckily he did. Tails saved Sonic and began shouting at him.
"What are you crazy? You almost got yourself killed", said Tails.
"Hey I aint losing these things again", said Sonic.
"Well I suppose it's OK. Anyway what do we do now?" asked Tails.
"I don't know. Hey how did you know to look for me here?" asked Sonic.
"Some guy gave me a note saying he saw you falling into this region. He must be at some observatory or something. He called himself MP", said Tails.
"Well we should go thank him", said Sonic.
Just then a huge crash could be heard and a tidal wave appeared. The two heroes looked to where they thought the crash happened. A huge Island had suddenly appeared out of nowhere.
"Could it be? Angel Island?" asked Tails.
"Angel Island?" asked Sonic.
"I heard stories about it when I was in the orphanage. Legend has it that the Master of the Emeralds sleeps there, normally holding the Island in the sky. I always thought it was nothing more than a story, but if it has fallen out of the sky it would explain that tidal wave", said Tails.
"It doesn't matter. Look at THAT!" said Sonic pointing at a huge black dome, just visible but mostly hidden by a mountain.
"The Death Egg? It survived re-entry and the crash?" asked Tails.
"I'm sure that's the Death Egg, which means this adventure isn't over. Take us to the Island", said Sonic.
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Before the crash, Knuckles, a red echidna had been exploring the Island he called his home. He knew little of why he was the only person on the island, but to be honest he didn't care. The Island had always stayed in the sky, hidden from the naked eye by mysterious clouds. His only real knowledge was a good knowledge of the English language and that he had to guard the Master Emerald.
Since no-one had come to the Island, he knew it was safe in the Hidden Palace. It was in a shrine under a volcano, completely hidden from the naked eye. He felt it was much safer there than on the primary shrine he found it at. His first memory was waking up in front of that huge Green Emerald, warm from the glow it gave, crying in hunger. Somehow he managed to get fed and taught by a mysterious voice. He didn't quite understand it but it happened.
He assumed it was the Emerald protecting its guardian somehow. It didn't concern him, as he grew up he found his own way to feed himself, the Island had it's fair share of tasty food scattered around. Moving the Emerald to the hidden shrine allowed him to search the island in peace. So many mysteries involving the Island, he had learned so much yet felt there was so much more. All the hidden pathways he had found must've had a purpose.
He spent all his spare time exploring the island, checking on the Emerald every now and then. During one of his searches he saw a huge black sphere headed straight into the jungle area behind the Ice Cap Mountains. He still didn't know how he knew that name, or any name relating to the areas of the Island. Hydrocity, Marble Garden, Ice Cap, Mushroom hill, Sandopolis, Lava Reef and the Sky sanctuary.
A shockwave of force knocked him off his feet as the black sphere crashed into the island. As he sprang to his feet he found the entire Island started to shake. It started to fall out of the sky for the first time ever.
Although there was many mysteries, one thing he knew more than ever was that the Master Emerald held up the Island. If the Island fell then there was something up with the Emerald. For the first time ever the Master Emerald was in danger.
He rushed through the tunnels back to the Master Emerald. It was difficult to get there but he managed. As it crashed in the ocean Knuckles froze in horror. The Emerald that had glowed with an intense green light barely shone at all.
"What is happening here?" asked Knuckles, "That thing that crashed into the Island! It's the cause for all this".
Knuckles made his way to the crash site as quickly as he could. He soon found himself at the crash site. The Black sphere was made out of some sort of metal, and the crash had smashed it into two large pieces. He found a large bald fat man trying to free himself from the wreckage.
"Who are you and what are you doing on my Island?" asked Knuckles.
The fat man shook his head and tried to recover from the effects of the crash.
"I am the great scientific genius Dr. Ivo Robotnik", said the fat man.
"Robotnik huh? So what's this thing Doctor?" asked Knuckles.
"It is the De…Life Egg. A place where sick people could be healed without fear of spreading a disease across the world", said Dr. Robotnik.
"Uh huh, and why is it a wreck? Why did it crash into my Island causing it to fall into the ocean", said Knuckles.
"Fall into the ocean? Is this…Angel Island?" asked Dr. Robotnik.
"Yes, now answer my question", said Knuckles.
"An evil Blue Hedgehog by the name of Sonic broke into the Life Egg and screwed up the orbit controls. It crashed back to Earth and amazingly found itself crashing into this once considered mythical island", said Dr. Robotnik.
"Mythical? Well I guess that's how people consider something that hasn't appeared in thousands of years", said Knuckles.
"The crash knocked the Island into the ocean? Interesting. How does the Island stay up in the sky anyway?" asked Dr. Robotnik.
"Sorry I can't tell you… I can hear a plane approaching", said Knuckles.
There was a brief silence.
"No, why can't he just leave me alone. That must be the Tornado, Sonic's plane. Please you have to stop him. I'm a scientist not a fighter, it's all down to you", said Dr. Robotnik, "Who knows what he's come to the island to do"
"You poor man. I'll take care of this little problem", said Knuckles.
Knuckles disappeared and Dr. Robotnik laughed.
"That fool, so easily tricked. I'll let him take care of Sonic while I find a way to restore the Death Egg. This Island is usually in the air. If I can find out how it can stay in the air without rockets I will be able to use it to launch the death egg again", said Dr. Robotnik.
Ok let's begin.