How about a crossover with the Legend of Zelda? Sonic could be transported to Hyrule. He'd find that his speed is both an advantage and a hindrance in this new world. The landscapes are much different from his usual zones. He might team up with Link to defeat Ganon who has somehow gotten his hands on some chaos emeralds and is using their power in a way that's corrupting Hyrule.
One idea could be a crossover with another Sega character like Bayonetta. Sonic could team up with her to fight against a common enemy that has the power to both slow down time (like Bayonetta's Witch Time) and manipulate the chaos energy in Sonic's world. They would have to combine their unique abilities to defeat this new threat.
A Sonic Unleashed and My Little Pony crossover fanfiction could be really fun. Sonic could end up in Equestria and have to use his super speed to help the ponies with a problem. Maybe a new villain has arrived that moves so fast the ponies can't keep up, but Sonic can. He'd also have to deal with the different magic in Equestria which could interact in strange ways with his chaos powers.
Maybe there's a strange energy rift that pulls Sonic into Megaman's world and vice versa. Sonic's speed causes chaos in Megaman's more structured world, while Megaman's weapon - based combat puzzles Sonic at first. However, they soon find out that there are common enemies that are trying to take advantage of the rift to gain power in both worlds. So they combine their abilities, like Sonic using his speed to help Megaman reach difficult areas, and Megaman using his blasters to clear paths for Sonic.
A cool plot might be that there's a strange energy surge that starts to merge their two worlds together. Sonic and Mega Man meet and initially misunderstand each other's motives. But as they figure out the cause of the energy surge, they realize they need to work together. Sonic's speed can help Mega Man reach places quickly, and Mega Man's weaponry can assist Sonic in combat against tougher enemies.
One idea could be a Sonic crossover with a superhero universe. Sonic's speed could be compared to the Flash's, and they could team up to stop a common villain who is trying to steal chaos emeralds and speed - force related items. Another plot could be a crossover with a fantasy world. Sonic meets magical creatures and has to use his speed to outrun dark magic. Maybe he teams up with a wizard or a fairy.
One idea could be Sonic and Infinite teaming up against a new common enemy that threatens both their worlds. Maybe a powerful alien force arrives, and they have to combine their skills and speed to defeat it.
Maybe Sonic discovers a chaos emerald has the power to transform Pokemon into super - powered versions, similar to Mega Evolutions. He has to work with Pokemon trainers to make sure this power doesn't fall into the wrong hands. The chaos emeralds' energy could also attract Legendary Pokemon, leading to some epic battles and adventures.
One idea could be a crossover with another popular game character like Link from The Legend of Zelda. Sonic the Werehog could find himself in Hyrule and have to team up with Link to defeat a common enemy. Maybe Ganon has somehow tapped into the power of the Chaos Emeralds and Sonic's werehog form is needed to counter it due to its unique strength and agility in that form.
One idea could be a crossover with another classic game series like Mega Man. Sonic could team up with Mega Man to stop Dr. Eggman and Dr. Wily who have joined forces. They'd combine their unique abilities, Sonic's speed and Mega Man's weaponry, to take on the evil duo in a world that combines the zones from Sonic Mania and the levels from Mega Man games.
Well, a cool plot for Mario Sonic crossover fanfiction might involve a new character that can travel between their worlds freely and is causing chaos. Mario and Sonic initially suspect each other but then realize they need to join forces. For example, this character could be stealing power - ups from Mario's world and Chaos Emeralds from Sonic's world to gain ultimate power. They would have to explore both worlds, facing their respective villains' minions along the way.
One idea could be that Mario and Sonic have to team up to save both their worlds from a new, powerful villain that is threatening to merge their dimensions in a chaotic way. For example, Bowser and Dr. Eggman could accidentally awaken an ancient evil while arguing over who is the better baddie.
One idea could be Sonic and his friends from the SatAM universe teaming up with characters from another Sonic series to defeat a new, powerful villain that threatens both their worlds. For example, they could join forces with the Sonic Boom crew. This would bring together different versions of Sonic characters with unique abilities and personalities, leading to some really fun interactions and epic battles.