A powerful warlock who wants to harness the powers of both Danny and Carrie for his own evil purposes. He could be an ancient being who has been waiting for the right time to strike when both Danny and Carrie are at their strongest.
It could be Sam and Tucker. Since Danny has become a villain, his former friends would likely try to stop him. They would be the main antagonists from Danny's point of view now. They would use their knowledge of Danny and their own skills to try and bring him back to the good side.
The main villain could be an older and more powerful version of Vlad. Maybe he has finally perfected his cloning techniques and created an army of half - ghost clones. He could be more devious and have a grand plan to take over both the human and ghost worlds.
Vlad Masters could easily be the main villain. Since he already has his own ambitions and a certain amount of power, in a royal - themed fanfiction, he could be trying to take over the ghostly royal throne. He might see Danny as a threat to his plans, especially if Danny has some newfound royal status, and thus plot against him.
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.
Perhaps a mad scientist from Danny's world who has somehow gotten access to Ultraman technology and is using it to create chaos. He could be creating mutant creatures that are a threat to both the Ghost Zone and Ultraman's world, and Danny and Ultraman have to stop him before it's too late.
A possible main villain could be a dark wizard from Star's world who has somehow gained the ability to control ghosts. He could use this power to try and take over both Danny's world and Star's, seeing the combination of magic and the ghost zone as a means to ultimate power.
It could be an evil scientist who has found a way to combine ghost and alien technology. He wants to use this to take over both the human world and the ghost zone.
Maybe the main villain is an ancient spirit that was once locked away in a dimension between the two worlds. Danny's accidental crossing of dimensions and Castiel's presence somehow break the seal. This spirit wants to destroy both the world of the living (that Danny protects) and heaven and hell (that Castiel is associated with) in order to create its own chaotic realm.
In a 'Danny Phantom becomes villain' fanfiction, it could be that Danny has a major falling out with his friends and family. He feels betrayed and abandoned. This emotional turmoil causes him to snap and turn to the dark side. He then uses his ghost powers to take revenge on those who he thinks have wronged him, becoming a feared villain in the process.
A group of human hunters who have decided to target Danny's ghost side could be the antagonists. They might be trying to capture Danny and use him for their own experiments. Danny, feeling violated and angry, decides to take revenge by using his ghost powers to outwit them at every turn, and expose their cruel intentions to the people of Amity Park.