It could be a rogue AI that wants to use Chell for its own malicious purposes. Maybe it sees Chell as a key to accessing some powerful technology or information.
One potential character could be a young hacker named Jin. Jin has some knowledge about AI but not as much as Chell will gain in the fanfic. He teams up with Chell to explore the deeper secrets of the AI world. Another character could be an AI ethics council member, Ms. Lee. Ms. Lee is constantly trying to ensure that the AI in the story are being used in an ethical way and she often clashes with Chell who is more interested in exploring the AI's capabilities without much regard for the rules at first.
Well, the fanfic could start with Chell being exposed to an experimental AI technology. This AI could start to influence her thoughts and actions in unexpected ways. Maybe it gives her enhanced cognitive abilities which she uses to explore a mysterious world. Along the way, she has to deal with the ethical implications of being so closely tied to an AI.
Well, in this fanfic, it could be that Chell discovers an ancient AI. The AI has unique powers and knowledge. Chell starts to learn from it and as she becomes more involved with the AI, she begins to change. She might gain new abilities or a different perspective on her world. For example, the AI could show her hidden secrets about the place she lives in, and together they could explore new areas or fight against some sort of oppression in her world.
Perhaps the fanfic focuses on Chell's character development as she becomes a core. It might involve her facing various challenges and obstacles that test her newfound identity. She could start off as an outsider but gradually gain the respect and recognition of the other elements related to the core through her determination and unique skills.
It could be Morgana. She might see Merlin's transformation into a dragon as a threat to her own power and plans. So, she tries to stop him from fully becoming a dragon or tries to use his new form for her own evil purposes.
It could also be a new villain that is specifically interested in Sonic because she is now a girl. Maybe a villain who has some sort of vendetta against female heroes or wants to use Sonic's new form for some evil experiment. However, Dr. Eggman is so iconic in the Sonic series that he would be a strong contender for the main antagonist role even in this fanfic scenario.
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.
Maybe the main antagonist is a group of demon hunters. They sense Ciel's transformation into a demon and see it as their duty to eliminate him before he becomes too powerful. They hunt him down relentlessly, making Ciel's life as a new demon very difficult.
It could be a rogue Pokémon trainer who wants to capture Ash - now as Pikachu - for his own collection. This trainer might have a cruel streak and not care about the well - being of Pokémon.