In a Danny Phantom and Ember time travel fanfiction, they could travel to different historical periods in the ghost zone. For example, they might visit the time when Ember first became a ghost. This would give Danny a better understanding of her backstory and might even lead to a change in their relationship. Or they could time travel to a point where the most powerful ghosts in the Danny Phantom universe were at war. Danny and Ember would have to choose sides or find a way to end the war without changing the balance of power too much in the present day.
One idea could be that Danny and Ember accidentally travel back to the founding of Amity Park. They could witness the early settlers dealing with strange ghostly phenomena and have to figure out how to not disrupt the timeline while also helping the settlers. Another plot could be that they travel to a future Amity Park that is overrun by a new type of ghostly threat, and they bring back knowledge to prevent it in their own time. Or they could travel to a time when Danny's parents were kids and see how their obsession with ghosts started.
One idea could be that Danny and Ember are forced to team up against a new powerful ghost enemy. During their time together, they start to see different sides of each other and feelings begin to develop. Another could be a time - travel plot where Danny goes back in time and meets a younger Ember, changing the course of their relationship. Or perhaps they get trapped in a dimension where they have to rely on each other for survival, and that closeness leads to love.
One idea could be that Danny and Sam travel back to the founding of Amity Park and accidentally change something small that has huge consequences in the present. For example, they might stop the first settler from building in a certain spot, which then changes the layout of the whole town and where ghosts can enter from in modern times.
A possible plot could be that there is a ghostly music competition in the Ghost Zone. Danny enters to stop some sort of dark plot related to it, and Ember is also a participant. Along the way, they form an alliance and their relationship blossoms as they work together to uncover the mystery behind the competition.
She could travel to different alternate timelines. For example, a timeline where Danny never became a half - ghost. Dani's presence in such a timeline could cause all sorts of chaos as she tries to figure out how to get back to her own timeline while also dealing with the differences in this new world.
One interesting 'Danny Phantom Danny and Ember' fanfiction could be where Danny and Ember team up to fight a new, powerful ghost that threatens both the human world and the Ghost Zone. They start off as reluctant allies but gradually come to respect each other's powers.
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 idea could be a story where Danny and Ember have to team up to defeat a new ghostly threat that is causing chaos in Amity Park. This could involve Ember using her music powers in new ways and Danny having to rely on her more than he expected.
A fanfiction could be set in an alternate universe where Skulker and Ember are the heroes and Danny Phantom is the villain. It would be interesting to see how their personalities and powers would be different in this reversed role situation.
One interesting fanfic concept is that Danny and Ember are forced to work together to save the Ghost Zone from a powerful, ancient evil. They must combine their powers and knowledge. Danny's scientific knowledge about the Ghost Zone and his powers, along with Ember's knowledge of the more mysterious and musical aspects of the Ghost Zone, could lead to a great adventure and a deepening of their relationship.