A great plot could involve Danny's friends from Amity Park coming to Gotham for some reason. They get caught up in one of Batman's cases. Danny has to balance protecting his friends, dealing with Batman's suspicions, and helping Batman solve the case which might be related to a powerful and evil ghost that has ties to Gotham's underworld.
One idea could be that Danny's ghost powers are misinterpreted by Batman as some new kind of meta - human ability. Danny might end up being hunted by Batman at first until they realize they can work together to fight a common enemy like a powerful ghost that has escaped into Gotham.
Maybe Danny accidentally gets transported to Gotham and his presence starts causing some strange paranormal activities. Batman, being the detective he is, tries to figure out what's going on. Danny has to hide his identity while also trying to find a way back home. They could form an uneasy alliance when they discover a criminal organization is trying to harness Danny's powers for evil.
One idea could be that Danny somehow gets transported to the Digital World. He uses his ghost powers in unique ways to survive and help the Digimon. For example, his intangibility might be useful against certain digital threats that the Digimon can't deal with on their own.
One idea could be that Skulker, instead of always hunting Danny, teams up with him to face a new and powerful ghost threat that is endangering the entire Ghost Zone. This would force them to put aside their differences and use their unique skills together.
Maybe there's a rift in the multiverse that connects the two worlds. Integra discovers Danny's powers and tries to recruit him to help in the fight against the vampires. Danny, being a hero in his own world, is hesitant at first but realizes the importance of cooperation when he sees the scale of the vampire threat in the Hellsing universe. He could use his intangibility and flight to outmaneuver the vampires while Alucard and Seras provide the heavy - hitting attacks.
Maybe Pandora has a powerful artifact that could help Danny in his fight against a particularly strong and evil ghost in his own world. Danny travels to Pandora to retrieve it, but he has to face many challenges there. The different ecosystems and magic on Pandora make it difficult for him to navigate, but he also meets some friendly creatures who help him along the way.
One plot idea could be that Danny Phantom is in Gotham City for some reason, maybe chasing a powerful ghost that has escaped into Batman's territory. He gets hurt during a fight with some of Gotham's villains who mistake him for a threat. Batman, being the detective he is, quickly figures out that Danny is not an ordinary 'meta' but a half - ghost. He helps Danny by providing him with a safe place to recover and using his resources to track down the ghost. Another idea is that Danny is hurt by a government agency that is trying to study his unique physiology. Batman steps in, using his influence to stop the agency from further harming Danny and helps him find a way to get back home to Amity Park.
One idea could be that Danny discovers a new ghostly power that he uses to take revenge on a group of bullies who have been tormenting his friends. He could use his intangibility in a creative way, like sneaking into their lockers and making their things disappear.
One idea could be Danny Fenton having to deal with a new ghostly enemy that can manipulate time, making his double life as Danny Phantom even more chaotic. Another could be Danny trying to balance his high school life, including exams and relationships, while also facing a ghost invasion that only he as Danny Phantom can stop. Or perhaps a story where Danny Phantom discovers a hidden power within himself that has a connection to his human side, Danny Fenton.
One plot idea could be that Fem Danny Phantom and Vlad have to team up against a new powerful ghost that threatens both their existences. This forces them to put aside their differences and work together, leading to a grudging respect for each other.
One idea could be that Danny has to face Pariah Dark again, but this time Pariah Dark has some new and unexpected powers. Maybe he has found a way to control the Ghost Zone in a different way that poses a huge threat to Danny and the human world. Another plot could be Danny trying to understand Pariah Dark's past to find a weakness. He could discover some ancient secrets about Pariah Dark's origin that no one else knew.
A possible plot is that a villain in the Infinite Stratos world discovers Danny's powers and tries to use them for their own evil purposes. Danny has to team up with the main characters from Infinite Stratos, like Ichika, to stop the villain. Along the way, Danny teaches them about the supernatural and they teach him about mecha piloting.