The main antagonist could be an ancient evil entity that has awakened. It sees the strong connection between Professor X and Storm within the X - Men and decides to swap their bodies as a way to start sowing chaos. This entity feeds on disorder and plans to use their swapped states to gradually destroy the X - Men from within.
It could be Mystique. She's always been one to cause trouble for the X - Men. Maybe she wants to disrupt the X - Men's operations by making Professor X and Storm swap bodies. She could use their confusion to her advantage, like stealing important information or causing internal strife among the team.
Well, one possible plot could be that due to a strange mutant power malfunction or a magical accident in the X - Mansion, Professor X and Storm swap bodies. At first, they'd be in a state of shock and confusion. Professor X in Storm's body would struggle to control her powers, while Storm in Professor X's body would have to deal with his telepathy. They'd have to work together to find a way to reverse the situation, all while trying to keep it a secret from the other X - Men to avoid chaos.
It could be a jealous colleague of Professor Pickle. This person might be envious of the time and attention he gives to Amy and tries to sabotage their work and relationship.
Maybe an akumatized version of a weather forecaster or a meteorologist. Frustrated by always being wrong about the weather or not being taken seriously, Hawkmoth akumatizes them. They then use their knowledge of the weather and new - found powers to create the perfect storm and cause havoc in Paris, making them a formidable antagonist for Ladybug and Chat Noir.
Another option is that it could be an existing character from their respective universes who has turned against them. For example, one of Lord Boxman's former robots that has gained sentience and now wants to destroy him and anyone associated with him, including Professor Venomous.
It could be a rogue Wakandan scientist who is jealous of the daughter's unique abilities. He might see her as a threat to his own plans of taking over Wakanda's technology and using it for his own evil purposes. So, he tries to undermine her at every turn and stop her from fulfilling her destiny in Wakanda.
It could be a powerful dark wizard from the Enchantress' world who follows her to the Naruto universe. He wants to capture the Enchantress and use her powers for his evil plans, and also sees the chakra in Naruto's world as a new source of power to conquer. He could have dark magic that can nullify ninjutsu, creating a real challenge for Naruto and the Enchantress.
Perhaps a powerful demon that has a grudge against the power of Amaterasu. It targets Naruto because he is the one who seems to be getting closer to Amaterasu. The demon could be from an ancient time when Amaterasu was first used to seal it away, and now it's back to stop Naruto from fully understanding and using Amaterasu.
Kawaki could also be a potential antagonist. If he feels that Delta's connection with Naruto is a threat to his own place in Konoha or his relationship with Naruto, he might act against them. He has a complex past and his insecurities could drive him to oppose their alliance.
It could be a rogue demon slayer who disagrees with Oyakata - sama's leadership and sees Tanjiro as a tool to undermine him. This character might be jealous of Tanjiro's closeness to Oyakata - sama.
Mephisto could also be a great main antagonist. His ability to corrupt and manipulate could pose a real threat to Naruto. Mephisto might try to turn Naruto's friends against him or corrupt Naruto himself. Since Naruto values his comrades highly, this would be a difficult situation for him to deal with. And if Mephisto manages to get into Naruto's head, it could lead to some really intense and dark moments in the fanfiction.