The Sentinels could also be the main villain in this type of fanfiction. They are often the symbol of mutant oppression. In a story about 'Termination', they could be upgraded to be even more powerful and relentless in their pursuit of mutants, causing the X - Men to face their toughest challenge yet.
Mr. Sinister would be a great main villain. He's always had his own sinister plans for mutants. In a 'Termination' scenario, he could be taking advantage of the chaos to further his experiments on mutants, seeing it as an opportunity to create more powerful mutants under his control.
A lesser - known mutant with a grudge against the X - Men could be the main villain. Maybe this mutant was rejected by the X - Men in the past and now, during the 'Termination' situation, they decide to take revenge. They could be using their powers in unexpected and dangerous ways to target the X - Men and try to bring them down.
Another idea might be a story where a powerful mutant turns against the X - Men in the context of 'Termination'. This could create a lot of internal conflict within the group as they try to deal with this betrayal while also facing external threats. Maybe the mutant has a different view on how mutants should co - exist with humans and decides the X - Men are getting in the way.
A new villain could be created specifically for this fanfiction. This villain could be a being that feeds on the chaos between the two different universes. It has the ability to disrupt chakra flow in Naruto's world and nullify magic in Lulu's world. Naruto and Lulu would have to figure out how to work together to stop this entity before it destroys both of their homes.
A group of mischievous imps could be the villains. They are envious of the beautiful things that Tinkerbell and the bubble can create together. So they play tricks on them, like creating false illusions to make Tinkerbell doubt the bubble and vice versa. Their goal is to disrupt the harmony between Tinkerbell and the bubble so that they can't use their combined magic for good in the fairy world.
It could be a mad scientist. The scientist has been researching ways to combine organic and electrical energy. He sees Pikachu as the perfect specimen and Samus as someone who will try to stop his unethical experiments. So he sets out to capture Pikachu and eliminate Samus.
It could be a rogue shinobi who has found a way to enter the Matrix world and wants to take over both the real world and the Matrix. He uses his ninja techniques combined with the power of the Machines to create havoc.
Kabuto could also be a main villain in this context. He might see the potential in the gloves to further his own power - hungry goals. He could try to manipulate Naruto into using the gloves in a way that benefits him, or he could simply try to steal the gloves when Naruto is at his weakest.
Obviously Naruto and Wolverine could be main characters. Wolverine's tough - guy attitude and his healing factor would contrast well with Naruto's upbeat and determined personality. Jean Grey could also be a main character. Her powerful telepathic and telekinetic abilities would be interesting to see in the Naruto world, especially when interacting with ninjas who rely on physical and chakra - based skills.
It could be an evil ninja who has somehow gained access to Gem technology. He uses the power of the Gems to enhance his own jutsu and becomes extremely powerful. His goal could be to take over both the Naruto world and the world of the Gems.
Dr. Wily could be the main villain. He might have found a way to travel through time or dimensions to the world of Mega Man X. He then uses his knowledge of Mega Man's weaknesses and combines it with new technology in the Mega Man X world to create even more powerful and devious robots.
It could be a giant lemon - themed monster that wants to turn the Pac - Man world into a lemon - only place. This monster might be jealous of Pacman's popularity and sees the lemon - themed transformation as a way to make everything his own.