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.
It could be some of the more aggressive monster characters. For example, the dog monsters might be territorial and see Frisk as an intruder, so they bully Frisk.
His older siblings, if he has any in the fanfiction. They could use their age and influence to protect Percy. Older siblings often have a natural instinct to look out for their younger ones. They could walk Percy to and from school, or have a word with the bullies to scare them off.
One possible plot could be that Sonic is bullied by a new group of antagonists in his world. They might make fun of his speed, saying it's not all that great and constantly tripping him up during races. Another plot could be that Sonic is bullied by some of the other characters who are jealous of his popularity. They start spreading false rumors about him, which makes some of the animals in the forest start to avoid him.
The bullies could also be influenced by their parents or the village's general perception of Naruto. If the adults in the village see Naruto as a troublemaker or a potential danger (maybe because of the Nine - Tails within him), the kids might pick up on that and bully him as a way to fit in with the adults' views.
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.
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.
Perhaps an older teacher or coach who has always had an eye on Kuroko's potential could step in as a savior. They could see the signs of bullying and use their authority to punish the bullies and provide support and guidance to Kuroko, helping him to grow stronger both on and off the court.
It could be some random students at Peter's school. Maybe there are those who are jealous of Peter's achievements in science or his closeness to his friends like MJ and Ned. They might start bullying him just to make themselves feel better or to fit in with a certain clique.
It could be one of Sonic's old enemies who found a way to transform into him. Maybe Dr. Eggman created a sophisticated robot that looks and acts like Sonic.
In fanfiction, it could be some of the Slytherin students. They might be jealous of Harry's fame as 'The Boy Who Lived' or his friendship with popular Gryffindors. Malfoy and his cronies are often depicted as bullies in the original series, so they are likely candidates in the fanfiction as well.