One idea could be that Sonic accidentally enters the world of Equestria Girls while chasing Dr. Eggman through a strange portal. He then teams up with the girls to stop Eggman from stealing the magic that powers their world. Another could be a race between Sonic and Rainbow Dash which gets interrupted by a common enemy.
In a Sonic and Equestria Girls crossover fanfic, a cool plot could be that a new villain emerges who has the ability to manipulate time. This affects both Sonic's world and the Equestria Girls' world. Sonic and the girls must combine their unique skills and powers. Sonic's speed could be used to quickly gather information across both worlds, while the girls' magic could be used to counter the villain's time - based attacks. They have to overcome their differences and learn to trust each other in order to save both their worlds.
Maybe there's a villain from the MLP world that follows them into the Equestria Girls world. The girls then have to team up with their Equestria Girls counterparts to defeat this villain. They could combine their different skills, like the pony Rainbow Dash's speed in the air and the Equestria Girls Rainbow Dash's skills on the track team.
One idea could be a crossover with another popular animated series like Steven Universe. The characters from Equestria Girls could visit Beach City and interact with the Crystal Gems. For example, Twilight Sparkle might be intrigued by Garnet's future vision ability and they could have a discussion about the nature of time and knowledge.
One idea could be an OC who is a new student at Canterlot High. She has a unique power related to music, like she can make people feel different emotions through her singing. And she gets involved in a battle of the bands where there's some sort of mystery or magic influencing the competition.
One interesting plot point could be the culture shock the Equestria Girls experience when they first arrive in Equestria. They might be amazed by the magic that is so commonplace there but strange to them. Another could be their interactions with the ponies. For example, they might have to learn new ways of communication and social norms.
One idea could be Sonic crossing over with another popular game like Mario. Sonic could find himself in the Mushroom Kingdom and have to team up with Mario to stop a new threat that combines the chaos emeralds and power - ups from both worlds. Maybe Bowser has teamed up with Dr. Eggman to create this chaos.
One interesting story could be about Sonic somehow getting transported to the Equestria Girls' world and having to team up with the girls to stop a new villain. Maybe he uses his speed to outwit the bad guy while the girls use their magic and friendship powers.
One idea could be a crossover where Shadow meets the Equestria Girls during a magical event in their world. Maybe he has to team up with them to defeat a common enemy that threatens both his world and theirs.
Maybe there's a device that combines the chaos emeralds' power with Chemical X. This causes a strange rift in the dimensions, bringing Sonic and the Powerpuff Girls together. They have to work together to reverse the effects of this strange combination. Sonic uses his speed to gather the scattered chaos emeralds, and the Powerpuff Girls use their powers to keep the villains from interfering.
One idea could be that Sonic accidentally enters Equestria where Rainbow Dash lives. They could then have a race to see who is faster in the new and unfamiliar terrain for Sonic. Rainbow Dash might be amazed by Sonic's speed and Sonic could be intrigued by Rainbow Dash's ability to fly while racing.
One idea could be a crossover where the Powerpuff Girls and Sonic team up to fight a common enemy like Dr. Eggman and Mojo Jojo who have joined forces. They could combine their powers and speed to outwit the villains.