Well, Sonic is the central figure. But other characters like Amy Rose could be important. She might be heartbroken to see Sonic turn dark and try to use her love for him to bring him back. There could also be some new characters created specifically for this fanfiction. For example, a mysterious character who has the power to either make Sonic darker or has the key to bringing him back to normal.
The main characters are probably Sonic and an alternate version of Sonic. There could also be other Sonic characters like Tails or Knuckles making appearances to support the Sonics in their rescue mission. But Sonic and his doppelganger would be at the forefront, using their speed and skills to achieve the rescue.
There could also be some new characters introduced in this fanfiction. Maybe a mysterious figure who has the power to control Dark Sonic or someone who has a connection to the origin of Dark Sonic. These new characters can bring fresh plot twists and new relationships to the story.
Sonic himself is always a popular character in this type of fanfiction. Whether it's Sonic from Sonic Boom or the modern Sonic, he's the central figure. Tails also tends to be popular as he's Sonic's sidekick in both versions. His intelligence and ability to create gadgets can play important roles in the crossovers.
Sonic himself is usually really popular. Whether it's the Sonic from Sonic X or Sonic Underground, he's the main hero and often at the center of the action. People love reading about his adventures and how he deals with the challenges in the combined universes.
Classic Sonic and Modern Sonic are the stars, of course. However, Knuckles can also be a very popular character in these fanfictions. His role as the guardian of the Master Emerald in the classic world and his continued importance in the modern Sonic universe make him an interesting addition. He can be the one who initially doubts the partnership between the two Sonics but then comes around. And Amy Rose is another character that often appears. Her feelings for Sonic, both Classic and Modern, can add a touch of romance or at least some emotional depth to the story.
Tails is very likely to help. He's Sonic's best friend and is super smart when it comes to technology. He could build a device to speed up Sonic's recovery or find a way to treat Sonic's injury. Amy is also a possibility. She's very caring and would do anything to make Sonic feel better. And Knuckles might help too. He's strong and could protect Sonic while he's recovering.
The interactions can also be based on mutual goals. Say there's a threat to both Sonic's world and Equestria. Sonic and the ponies would have to communicate and combine their strengths. Sonic could use his speed to scout ahead and the ponies could use their magic to hold off enemies. They might also share their knowledge with each other. Sonic could teach the ponies about technology from his world, and the ponies could teach Sonic about the magic spells and potions that exist in Equestria.
Sonic, of course, is a must - have. But also Knuckles from both universes. In Sonic Boom, Knuckles is a bit more of a muscle - brained character in a fun way, while the classic Knuckles is more serious about guarding the Master Emerald. When they meet, there could be some hilarious misunderstandings at first, like Sonic Boom Knuckles trying to show off his strength to the other Knuckles, but then they end up teaming up against a common threat.