On random occurrence, Eggman has the genius idea to make a clone of Sonic. Through the use of Sonic's DNA, Eggman could create his own Sonic in his lab (one of them he has lying around), thus the creatively named "Clone Sonic" was created. Eggman took a page out of Gerald's book and used Chaos Drives for life support as otherwise the clone wouldn't be able to stay alive for long, it was just barely enough to keep it alive.The use of the Chaos Drives had the side effect of making the Clone Sonic have yellow quills. Eggman gave him a red hat and bowtie just so he could identify it, no deep reason for it really (convenient I know).
The clone would end up not really doing much, it didn't know how to use any of Sonic's moves and had basically no battle experience of any sort. Eggman, disappointed with the outcome, would end up abandoning the Clone Sonic in a warehouse at one of his bases. The clone stayed there for many years, its body decaying overtime while the chaos energy would take over more and more, his eyes glowing green, his accessories turned green too.
After Mario and Sonic at the Unnamed Sporting Event, Eggman would end up taking DNA samples from Sonic, Mario, Yoshi and Tails. He had planned to once again create clones, but this time he was confident he could do a much better job after having read Gerald's Journal, creating Shadow Androids, among other things.
Eggman creates the clones in his lab, not requiring the use of Chaos Drives any more, he was far better at creating life forms than in his younger years. He would implement all the Clones with mind control chips, in case they decide to turn on him (sentient life forms can be quite unpredictable). He could use said mind chips to train the clones on how they should act and train them for his newest scheme... a new Theme Park:
SONIC & MARIO's HERO PARK
There's Rides, Games, Music, Shows, Food, and that's about it... I mean what more could you need ? The main attraction of course, was the "heroes"(or the clones of them at least).
Clone Sonic, he loved to sing and play the guitar.
Clone Mario, he put on incredible magic shows for people.
Clone Yoshi, he told stories from long ago and cooked delicious treats for people.
Clone Tails, he had a weird hyperfixation on pirates for some reason... So uh, boats it is.
Eggman would disguise himself and go by a new name... Namgge (300 IQ). This way he could run his business while concealing his true identity from Sonic & Friends. To "ensure safety" in the park, Eggman had set up his trusty not Egg Pawns as security guards... but of course he needed people for the night shift, which was where his devious plan would show itself. He put posters, hiring night guards. Luigi would be the first person to get hired for the job, but after 1 night he ran out and was too scared to ever go back. Luigi screaming and running out would catch the attention of Amy Rose, from there she would see the park and be curious about it, so she decided to apply for the job.
After testing her luck for 5 nights, the clones get the best of her and she dies. The evidence of a murder happening would be cleared up quickly, her corpse would be left in a secret basement lab under the park where Eggman monitored everything from the inside and outside of the park. Eggman congratulates the clones on their victory. Their urge to murder is overwhelming, but they are held back due to the mind chips Eggman had installed.
During a crowded evening at the Park, the memory chips would suddenly malfunction. The clones, now free from the Doctor's control, started to slaughter all the visitors to the park. Eggman was panicking and instantly gets his security Egg Pawns to stop them while he heads to his emergency safe room. Once he gets there he takes a moment to breathe, but the clones were just at the door. He wasn't fast enough and was killed. The mass slaughter gets the attention of G.U.N and the clones are taken care of and heavily damaged. They are held in the basement and the park is under heavy surveillance as people have been told to evacuate the general area.
After some days, Sonic and Mario arrive at the scene, along with Tails and Yoshi. With the permission from G.U.N they are let into the park to investigate. The scene was disturbing to see, it was full of corpses, from visitors to G.U.N soldiers. Tails notices the several Egg Pawn parts and deducts that Eggman was involved. The gang split up to look around for more clues.
Following Sonic, he finds an office with a working camera system and he sees his friends on the cameras. As he keeps watching they eventually start disappearing, leaving Sonic worried, but he'd eventually find his friends again... in some strange outfits and they looked hurt too (it's actually the clones).
On the third hour there he'd see himself. Now he was sure these guys were something caused by Eggman.
After defending himself for 4 grueling hours, he looked at the cameras for longer, only to see his clone being decapitated by a yellow hedgehog, who then stared right into the camera and teleported, like some sort of Chaos Control.
After an hour of surviving against this yellow imposter, Sonic had enough and decided it was time to bring the whole place down. He would search around as fast as he could, until he found the basement. He saw his friends dead: Mario, Yoshi, Amy, Tails. Sonic teared up, but he couldn't stand there crying, he had to finish this once and for all. He scrambled about and pressed a button, activating a self-destruct sequence with the lights blaring red. With no time to waste, he ran out to escape but was quickly stopped by the yellow hedgehog.The hedgehog held Sonic by the neck, ready to kill him, but Sonic wasn't done fighting. He held the hedgehog down, ready to sacrifice himself as the whole park collapsed in a big explosion. The entire park was left up in flames... Sonic had died.
A few days had passed since the explosion. Clone Sonic MK 1, now turned into a dark smoky figure, found Eggman in the safe room waiting for rescue from his Badniks. During the clones' attack on Eggman, he actually didn't die, instead he was left unconscious for days and heavily wounded, but just barely managed to survive. Eggman was shocked to see this shadowy figure. He was scared and pleaded for the figure to leave him alone.
"Don't you remember, Doctor? IT'S ME" (roll credits)
Clone Sonic discusses his plans for a bigger and better theme park, and Eggman is forced to go along with it. Eggman questions how that would even be possible, so Clone Sonic creates a portal to go back in time and start anew. Unbeknownst to them, Luigi was watching the whole thing. He was there to mourn over his brother's death but now he knew he could avenge him, so headed toward the portal after the duo.
In the distant future, Eggman Nega decides to make a theme park with clones. Family tradition I guess.