>Sonic finds himself in ancient aquatic ruins, the writings on them too eroded to read. But he has the idea to go back in time and find the people who made them. However, upon reaching the past, he finds it's also deserted. However, he can now read the inscriptions, which tell how the Time Stones made Little Planet go back and forth through time, keeping it mysterious and untouched, allowing those who lived there to live in peace from the Earth below. But these writings are not yet old. Sonic wonders what happens to those who wrote them, when suddenly, he runs into Metal Sonic, stepping on an animal. Sonic stops in his tracks, only to realize it's not the real Metal Sonic, but just a hologram. Sonic destroys the hologram, and a few small animals come out of hiding. Eggman explains that he arrived and used Metal Sonic to capture most inhabitants of the planet. When they saw Sonic, they must have thought he was the same guy who captured their friends, so they hid from him. It was the perfect way to keep them from helping Sonic. Of course, as they talk, they're fighting, and Eggman's arrogance and laughter at his own plan allows Sonic to destroy his current machine, sending him flying off.
>Sonic is now more determined than ever to defeat Eggman, so he speeds through the next zone before finding Eggman and demanding to know what Eggman did with all the animals he captured. Eggman explains that Sonic already found them on his space station, when they fought in space, but that they'll have a hard time getting back to their own times considering Eggman has all the Time Stones. Sonic reveals that he has three Time Stones already, shocking Eggman, who thought hiding them in the Special Stage with his UFO machines guarding them would keep them protected. His shock allows Sonic to destroy his current machine, and send him flying away.
>The next area, Wacky Workbench, is utopic paradise in the past, with more evidence of the culture Eggman is destroying. Sonic finds a statue of an angel, but as he warps to the future, the statue turns into a statue of Eggman. Upon finding Eggman again, Sonic demands to know where Amy is, and questions why Eggman would even capture her. Eggman explains that he didn't get rid of all the animals on the planet just to let Amy run around freely. Plus, the irony of her getting captured by Metal Sonic was too great to ignore. Sonic attacks Eggman again, demanding to know where Metal Sonic and Amy are. Eggman, injured, points to a city with a giant statue of himself in the center, in an attempt to get Sonic to leave him alone and let him escape. Sonic runs down the star-lit speedway to the center of the city. As he runs, he looks at the moon, and finds a large chunk of it blasted away, reminding him that this is the bad future that will happen if he doesn't stop Eggman.
>As he approaches Eggman's base in the center, Metal Sonic catches up beside him, and they race toward the base. Of course, Sonic wins, passing through the doors and shutting them just in time for Metal Sonic to crash into them and explode. Sonic finds Amy tied up and frees her, telling her to stay here while he deals with Eggman, and that he'll be back in a flash.
>Sonic runs into Eggman's base, but before he can confront the doctor one final time, he gets hit by a laser that shrinks him. He finds Amy at the entrance of the base and tries to ask her for help, but he's too small to get her attention. Instead he powers forward to the heart of the base, figuring that he can't let this stop him anyway. After an adventure dealing with giant enemies and traps, Sonic finds the growth-ray just in time to defeat Eggman and destroy his base, freeing Little Planet.
>As Eggman's machines self-destruct all over the planet, Sonic speeds past Amy, whisking her off her feet, and carrying her backwards through the zones and down the giant chain back to Earth just in time for the chain to fall apart, freeing Little Planet and letting it disappear. Amy thanks Sonic for saving her, thinking that this confirms they're meant to be together, but as she leans in for a kiss, he seemingly doesn't even notice, speeding off before she can say another word.
Again, this definitely wouldn't be more than three issues. One issue would cover the intro/Palmtree Panic/Collision Chaos, one for Tidal Tempest/Quartz Quadrant/Wacky Workbench, and one for Stardust Speedway/Metallic Madness/ending. About seven pages each zone would be enough, since you'd want this to be a rather fast paced series.