"I have got to stop leaving my candy in mysterious caves!" Eggman said to himself as he floated around in what the author assumes is called the Egg Flyer. "Wait, is that my candy?" A mechanical arm came out from the Egg Flyer and grabbed a stone tablet. "No, it's just some prediction about the Chaos Emeralds-Wait! I can use this to rule the world!" Eggman ran to his Egg Carrier, went to Angel Island, and broke the Master Emerald.
"Oh, here's my candy, it was in the Egg Carrier the whole time!"

Meanwhile, Sonic was passed out on a beach chair showing no signs of waking up soon when Tails crashed his plane. He suddenly jumped over the pool and ran to the beach. In a little more than 3.05 seconds, Tails had been rescued.

"What happened? You're way too good of a pilot to crash!"

"Well, using my newfound genius-ness, I decided that Chaos Emeralds can power planes!"
"Can't argue with that."

"But Chaos Emeralds are highly unstable, which is why I'm going to give THIS," Tails held out a purple Chaos Emerald. "To Eggman the first chance I get."

Sonic stared. "Okay, I'm gonna go steal that golden chao egg from the antique shop."

"Alright!" Tails left. "Come to my new genius house! I want you to see my new sofa!"

In the Mystic Ruins, either Sonic or Tails fought the Egg Hornet. (nobody was quite sure who actually fought it)

"Here you go, Eggman. I was going to get it wrapped, but you can have it now." Tails held out the previously mentioned Chaos Emerald.

"CHAOS!" Eggman yelled.

"What's going on? Are you in pain?" Sonic asked. A gloopy blue thing came out of the ground and ate the Chaos Emerald out of Eggman's hand. It then grew bigger and turned into a gloopy blue puddle and soaked back into the ground.

A few levels and ten hundred trips to the Chao Garden later, Sonic, Amy, and Tails were on the Egg Carrier. "Tails, go take Amy on a date or something, I'm gonna go kick Eggman's dumb butt!"

Tails flew away with Amy. Sonic prepared to fight the gloopy blue thing when Big the Author's Favorite Character defeated it instead and saved his pet frog.

"Hm, I feel a strange combination of admiration and annoyance. Anyways, I'm gonna go kick Eggman's dumb butt!" Sonic did so.

Later...

"It's time for SUPER SONIC!" Sonic flashed yellow for a second but then a record scratched on the epic music in the background and he turned normal again.

"We must use the combined power of our hearts to repower the Chaos Emeralds!" Everybody concentrated really hard.
"Augh, heart attack!" Knuckles was immediatly rushed to the only hospital that wasn't submerged in water. The Chaos Emeralds now had all their positive energy back.

"It's time for SUPER SONIC!" This time Sonic properly became SUPER, frizzy hair and all. He then proceeded to kick the God of Destruction's (that wasn't really gloopy anymore) butt.

"Are you Sonic the Hedgehog?" A man asked.
"The one and only."

"I'm from the city goverment. We're blaming you for flooding the city. You now need to pay the city one zillion rings."

"Aw..."