The ghosts that were usually the antagonists could become the protagonists. For instance, Vlad Plasmius could be in a role where he's trying to protect the human - ghost balance instead of causing chaos. He could have a group of human sidekicks who help him in this new role, and they could be characters like Paulina or Dash who have had a change of heart.
A new character could be introduced as the main character. Maybe a human who has the ability to enter the ghost zone freely and has to deal with the role - reversed situation. This character could befriend some of the ghosts who are now in a more vulnerable position in the human - dominated world and together they try to restore the original order.
Danny's parents could be main characters too. They might be trying to throw Danny a normal human birthday party, completely unaware of the ghostly happenings that often surround their son. Their attempts to have a 'normal' celebration could be constantly interrupted by Danny having to slip away to deal with ghost problems. This would create an interesting dynamic between Danny trying to keep his double life a secret from his parents while still enjoying his birthday with them.
Obviously, the main character would be Danny Phantom himself, but in two different forms or versions. One would be the original Danny Phantom from the canon source, and the other would be a version created by the fanfiction. There might also be his friends like Sam and Tucker who could play important roles in helping the two Dannys understand each other and deal with any issues that arise from their meeting.
Besides Danny, the main characters could include some of the friendly ghosts from the Ghost Zone. They could be like Danny's support system in this new motherhood journey. Also, the school bully Dash might be in the story. He could start off making fun of Danny but then gradually come to understand and respect Danny's new role. And there could be a mysterious ghostly figure that either helps or hinders Danny in his newfound motherly duties.
One idea could be that the ghosts are the ones protecting Amity Park from the human villains. So, instead of Danny fighting ghosts, the ghosts are using their powers to keep humans with bad intentions at bay. For example, they could use their intangibility to stop burglars from breaking into houses.
In addition to the ghosts, there might be some human characters that are important in the 'phantom city danny phantom fanfiction'. They could be Danny's friends or family members who get involved in the events of the Phantom City. Their reactions to the supernatural world and their interactions with Danny and the ghosts would add an interesting dynamic to the story.
Obviously, Danny would be the main character since he's the one getting sick. His friends, Sam and Tucker, would also play important roles. They would likely be the ones trying to help Danny get better and keep his secret if he doesn't want it known.
Definitely Danny's kids if he has any in the fanfiction universe. They could inherit his powers and have to learn how to use them while dealing with their own personal issues. Also, Sam and Tucker's children could be main characters. They might not have ghost powers but could be very tech - savvy and help in other ways, like creating new gadgets to fight ghosts.
Obviously Danny Phantom himself would still be a main character. His friends like Sam and Tucker would likely also be important. They've probably grown and developed new skills over the 10 years.
Danny would be one of the main characters, no doubt. And from the Sekirei series, Musubi could be a key character in the fanfiction. She is one of the more prominent Sekirei, being kind - hearted and strong. Her naivete might lead to some humorous situations when she first meets Danny. Also, Tucker Foley from Danny Phantom could be another main character. He could use his tech - savvy skills to help in the Sekirei world, perhaps by creating some new gadgets that work in that universe as well.
Danny's parents could also be part of the story in an interesting way. Their obsession with ghosts might accidentally interfere with Danny's attempts at romance. For example, they could set up some kind of ghost - hunting event that gets in the way of Danny's date, or they could unknowingly chase away Danny's love interest if she has any ghostly traits that they misinterpret as a threat.