A new character could be created as the main villain. For example, a corrupted spirit from Kagome's world that has the ability to possess the Transformers. This entity could use the Transformers' strength and technology for its own evil purposes, causing chaos in both worlds. It would be a formidable foe as it combines the magic of Kagome's world with the mechanical power of the Transformers.
The Fallen could also be the main villain in this fanfiction. He might see Kagome's presence as a disruption to his plans for universal domination. He could try to eliminate her while also using the chaos caused by her appearance to further his own goals against the Autobots. He might also try to corrupt Kagome's magic for his own use, which would put her and the Autobots in a very difficult situation.
One possible plot could be that Kagome accidentally stumbles into the Transformers' world through a magical portal. The Autobots initially mistake her for a threat but soon realize she's an ally. Together, they could fight against the Decepticons who are trying to use Kagome's knowledge of magic to gain an upper hand in their war.
It could be a demon who has a grudge against Kagome's father. Maybe her father defeated this demon long ago, and now that Kagome is in the picture, the demon sees it as a chance to get revenge on the family.
Perhaps a rogue ghost who has managed to hack into Cybertronian technology. This ghost, let's call it Techno - Ghoul, has the ability to possess and control Transformers. He starts causing chaos by making Autobots and Decepticons fight each other. Danny Phantom has to use his ghost - hunting skills and his knowledge of both the human and ghost worlds to find a way to exorcise Techno - Ghoul from the Cybertronian systems.
It could be Naraku. Even though the focus is on Kagome and child Bankotsu, Naraku is always lurking in the shadows in the Inuyasha universe. He might see Kagome's interaction with Bankotsu as a threat to his plans and try to manipulate the situation to his advantage. He could try to turn Bankotsu against Kagome or use Kagome's distraction with Bankotsu to carry out some other evil deeds.
The Decepticons would be an obvious choice. They are the natural enemies of the Autobots and could pose a great threat to Dante as well.
Lex Luthor would be a great choice. He's Superman's long - time nemesis. He could form an alliance with some of Batman's foes like the Joker. Luthor could use his intelligence and resources to create a plan that only Superman and Batman together could stop.
Well, in 'Dante meets the Transformers fanfiction', Dante is the main character. He is the one who is going to have the encounters with the Transformers. He will bring his own story, his own set of skills and personality into this fictional meeting. The Transformers are important too, but Dante is the one through whose eyes we will probably see most of the action and development in the story.
Megatron would be a classic choice. His desire for power and domination could put him in direct conflict with Christopher Stratos. He might see Christopher as a threat or an obstacle in his plan to conquer the universe or gain control over some powerful Transformer technology.
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.
Maybe the Riddler. He could set up a series of elaborate riddles that not only challenge Batman but also the curious kid OC. The kid's fresh perspective might actually help Batman solve the riddles faster and catch the Riddler before he executes his grand plan.