It could be a character who is against the idea of Percy being a girl. Maybe someone who believes in strict gender roles in their world and sees Percy's transformation as an abomination. For example, an old - fashioned wizard or a powerful deity.
There could be a group of poachers who are not just after regular game but are also involved in some dark magic. They oppose the hunters and especially Percy when he tries to stop their illegal and dangerous activities. They might have powerful backers or magic items that make them a formidable foe for Percy and the other hunters.
Perhaps it's one of Percy's former friends who has turned against him. This friend could be jealous of Percy's powers or has been influenced by some dark force. Their actions and taunts could be what drives Percy to become dark, making them the main antagonist in the story.
There could also be new antagonists. For example, some of the more traditional wizarding families who are against the idea of a female Harry. They might see her as a threat to the old - fashioned ways of the wizarding world and try to undermine her.
It could be Vilgax. He might see Ben 10's new form as a weakness and try to take advantage of it.
It could be an ancient and powerful god who has long been plotting against Percy. This god might be jealous of Percy's power and popularity, so he devises a plan to turn Percy into a killer, knowing that it will lead to Percy's downfall and his own rise in power.
Another possibility is that an alien race that Ben has previously encountered and thought was friendly, now turns against him/her because of the change in gender. They might have some strange beliefs or customs that make them view Ben's new form as a threat or an abomination, and thus they become the main antagonists in the fanfic.
Perhaps an old acquaintance of Ryuuji's who has some unresolved issues with him. When Ryuuji turns into a girl, this person sees it as an opportunity to get revenge in a more devious way. They might try to manipulate the situation and the people around Ryuuji to make her life miserable, all while hiding their true motives from others.
It could be the warden of the prison. The warden might be a cruel and power - hungry person who wants to keep Percy imprisoned for his own reasons, like getting some sort of reward or power from those who put Percy there.
A powerful dark sorcerer could be the main antagonist. He might be seeking to use Percy's skills for his own evil purposes, and when Percy refuses, he becomes the target. The sorcerer would have a vast array of dark magic at his disposal, making him a formidable foe.
It could be an evil spirit that wants to use Naruto's new ghostly form for its own dark purposes. Maybe it tries to control Naruto and make him do evil things.