A power - hungry politician in Nero's world could be the main antagonist. They see Nero as a threat to their power or as an easy target to gain more influence. They manipulate situations to make it seem like Nero has done something wrong.
Well, it could be that Nero accidentally breaks some important rule in his world. Maybe he accidentally damages a powerful relic that is crucial for his community's safety, and then he has to face the wrath of the elders or those in charge.
Maybe an evil artist from another dimension. This artist is jealous of Nathanael's pure creativity and the unique power of his miraculous. They come to Nathanael's world to steal his ideas and use his miraculous for their own dark purposes, like creating chaos and destruction through art.
Maybe the main antagonist is an old enemy of Robin's who becomes jealous of his new powers. This enemy then devises a plan to steal Robin's powers or at least neutralize them so that he can regain his former status as the top threat. He could be a powerful martial artist or a criminal mastermind with a large network of henchmen.
It could be a jealous rival. This rival might be envious of mankae's popularity or achievements. So, they set him up to get arrested by providing false information to the police. They want to see mankae's downfall and think that getting him arrested is the best way to achieve this.
It could be Orochimaru. Since he has always been interested in powerful ninja abilities, he might see Sakura with the Sharingan as a new target. He could try to steal the Sharingan from her to add to his own collection of powerful jutsus and abilities.
Maybe it could be a mad scientist who wants to study the chibi. He sees it as a unique specimen and is willing to do anything to get his hands on it.
It could be a new villain created specifically for the fanfiction. Maybe someone who has a vendetta against Chloe and targets her because she has the Miraculous.
A rogue robotic entity could be the main antagonist. This entity has the ability to roboticize other beings and views Tails as a prime target. It wants to use Tails' body as a vessel to spread its robotic influence further, so it sets out to roboticize him and then use him as a tool for its own dark purposes.
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 Sasuke. I know they are friends in the original, but in this fanfiction, Sasuke might turn against Naruto for some reason. Maybe he becomes jealous of Naruto's newfound power or status.