Dr. Eggman could be the antagonist. He's always trying to defeat Sonic, and shooting him could be part of one of his evil plans. Maybe he developed a new weapon specifically designed to take Sonic down.
It could be a lone wolf type of character. This person is a survivor in the same world as Clementine but has gone a bit crazy from all the hardships. They see Clementine as a competitor for resources and decides to shoot her to get rid of the competition.
Another possibility is a corrupted version of one of Sonic's friends. Maybe through some dark influence, like an evil Chaos Emerald, a friend turns on Sonic and blinds him. This would add an extra layer of drama as Sonic has to deal not only with his blindness but also the betrayal of someone he trusted.
One possible scenario could be that Sonic is shot by a robotic enemy while trying to protect his friends. He might then have to rely on his friends to get him to safety and find a way to heal his wound. Another could be that he's shot by a misfiring weapon of a friendly character, leading to a lot of guilt and a race to save Sonic's life.
It could be a rogue agent from their own organization. Maybe someone who has a grudge against Washington for some past event. This person might see Wash as a threat to their own plans and decides to take him out.
It could also be a new villain. Maybe someone who has been waiting for Sonic to be in a vulnerable state. This new villain could have a special power or weapon that is more effective against Sonic as a kid. For example, a device that can slow down Sonic even more or nullify his powers temporarily. They might target Sonic not just because of his weakened state, but also because they know that his friends will be distracted trying to help him get back to normal.
Perhaps a mysterious stranger who has some unknown vendetta against the Heartland family. This person could have been lurking around the ranch for a while, waiting for the perfect opportunity to strike. Or it could be someone within the community who has a hidden agenda and sees Amy as an obstacle to their plans.
I'm not sure specifically as there could be various interpretations in such a fanfiction. Maybe Metal Sonic sets Sonic up in a way that makes Sonic look bad to the other characters, perhaps by faking some evidence or causing chaos and making it seem like Sonic's fault.
Eggman Nega could be a great main antagonist. He has the intelligence and the desire for power. He could find a way to open portals between the Sonic X and Sonic Boom universes to steal resources and technology from both. His plans would force Sonic X's Sonic and Sonic Boom's Sonic to team up against him. He could use his robotic creations from both universes, combining the advanced tech from Sonic X and the more rustic, yet effective, machines from Sonic Boom.
Positive Sonic fanfiction could be about Sonic mentoring the younger characters like Tails and teaching them important life lessons. Or it could be about Sonic and his friends having to solve a mystery in their world, like a strange disappearance of an important item or character. Fanfictions that show the characters growing and evolving in positive ways, such as Amy becoming more confident in her own abilities, are also excellent alternatives to inappropriate fanfiction themes.
Another possibility is a new character. This new character could be causing trouble between Sonic and Tails. For instance, the new character might be spreading false rumors about Tails, which makes Sonic angry at Tails.