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.
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.
It could be a jealous rival detective who wants to get rid of Sherlock to gain more fame in the detective world.
It could be a dark wizard who has a vendetta against Fairy Tail. Maybe someone who Natsu defeated in the past and is now seeking revenge.
It could be a new villain who has a vendetta against Tony. Maybe this villain has some past connection to Tony that we don't know about yet, and they finally take their chance to harm him by shooting him.
It could be some of the lesser - known badniks that team up to bully Sonic. Since they can't defeat him on their own, they figure that by ganging up on him and bullying him, they can at least make his life difficult.
One possibility is Dr. Eggman. He has always been after Sonic and wants to stop him. Kidnapping Sonic would be a way for him to achieve his evil goals.