The Joker could be a great villain. Imagine him getting his hands on some ghostly technology or artifacts from Danny's world. He would use it in his own chaotic and unpredictable way, causing mayhem in Gotham and also attracting Danny's attention. Danny and Batman would have to work together to stop the Joker's mad schemes.
Maybe a mad scientist who has found a way to combine ghostly energy with his own technology. He targets Danny to use him as a power source for his evil experiments. Batman gets involved when he notices the strange energy signatures in Gotham. The scientist would be a formidable antagonist as he has both scientific knowledge and the power of the ghosts on his side.
I think Superman would be the most likely. Superman is known for his kind heart and open - mindedness. He would probably see Danny as a young hero in need of some guidance and friendship. He wouldn't be too quick to judge Danny based on his ghostly appearance or powers.
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.
Harley Quinn is an obvious choice. Her obsessive love for the Joker could be transferred to Batman in a fanfiction harem scenario. She's unpredictable and could add a lot of chaos and humor to the group. Then there's Poison Ivy. Her connection to nature and her alluring charm would make her a likely candidate. She could use her plants to protect the harem or create a private sanctuary for them.
I think Eobard Thawne, the Reverse - Flash, could be really interesting. He could use his speed to try and steal Danny's ghost powers. His devious nature and time - traveling abilities would make him a formidable foe. He might see Danny's powers as a way to enhance his own and become even more powerful. And Danny would have to use his unique ghostly skills, like his ability to phase through objects and fly, to outwit the Reverse - Flash.
Vlad Masters could be a likely antagonist. He might see Kim as a threat to his plans regarding Danny. Since he's always looking for ways to get Danny on his side or out of the way, he could try to use Kim as a pawn. Maybe he tries to manipulate Kim into thinking Danny is the bad guy, or he uses his ghost powers and wealth to create problems for both of them.
I think Sam from Danny Phantom would get along well with Black Widow. They both have a no - nonsense attitude and are strong - willed. Sam could teach Black Widow about environmental protection, and Black Widow could train Sam in more hand - to - hand combat skills. Also, Tucker might be an ally to Iron Man. Tucker's love for technology and his skills in that area would make him a great partner for Tony Stark. They could collaborate on creating new gadgets that combine Danny's ghostly technology with Stark's high - tech creations.
I think there's no clear - cut winner in a 'danny phantom vs justice league' fanfiction. Danny Phantom is a powerful ghost - hero in his own right. He has unique powers that the Justice League may not be familiar with at first. But the Justice League is a team of some of the most powerful heroes in the DC universe. If the story is written in a way that Danny has some sort of ace up his sleeve, like a new power or a powerful ghost artifact, he could potentially defeat the Justice League. On the other hand, if the Justice League is well - prepared and uses their combined skills effectively, they could overpower Danny.
Lex Luthor. He's always looking for a way to take down Superman, and an apocalypse would be the perfect time for him to make his move. He could be using the chaos to build some sort of doomsday device or manipulate events to his advantage.
Darkseid is another option. His power and his desire to conquer Earth could bring Batman and Superman together. He could target both Metropolis and Gotham, and his presence would require the two heroes to combine their skills. Batman's strategic mind and Superman's brute strength would be needed to face this powerful foe.