Well, one possibility could be that Natsu is forced to join Phantom Lord due to some dark magic or a powerful enemy's scheme. He might initially resist but then find some hidden good in the guild members.
Perhaps Natsu joins Phantom Lord in order to spy on them for Fairy Tail. He pretends to be a new recruit but is actually there to gather information about their evil plans and stop them from within.
The master of Phantom Lord himself could be the main antagonist. He might see Natsu as a threat to his power within the guild or have some vendetta against Natsu's old guild, Fairy Tail.
Well, it could be about Lucy initially being a spy for Fairy Tail in the Phantom Lord guild. Maybe she discovers some dark secrets within Phantom Lord that could either help Fairy Tail or put her in great danger. She might also form unexpected friendships with some of the Phantom Lord members while still remaining loyal to her Fairy Tail comrades at heart.
Well, one possibility is that Natsu could join Fairy Tail in a different way than in the original story. Maybe he has some special mission before officially becoming a member. For example, he has to prove his loyalty by helping an elder member with a personal problem.
One possible plot could be that Killua joins the Phantom Troupe in order to protect Gon. He might think that by infiltrating the troupe, he can keep Gon safe from their potential threats. Maybe he initially pretends to be on their side, but as time goes on, he starts to question his own actions and the morality of the troupe.
One possible plot could be that Natsu has been living a different life away from Fairy Tail. Maybe he was raised by another guild unknowingly. When he finally joins Fairy Tail later, he has to prove himself to the existing members who are skeptical of his late arrival. He might have unique magic skills he developed elsewhere that surprise everyone.
One possible plot could be that Natsu and Mirajane join Fairy Tail at different times. Natsu might bring his usual enthusiasm and powerful fire - based magic. He could quickly get into all sorts of adventures, making friends and enemies alike. Mirajane, on the other hand, could use her Take - Over magic to be a great asset in battles. Their joining could lead to new team - ups within the guild, like Natsu and Mirajane going on a mission together to stop a dark wizard who is causing chaos in a nearby town. They'd face challenges, but their combined skills would help them overcome the odds.
Well, it could be about Danny's powers being a great asset to the Young Justice team. Maybe he helps them with his ghostly abilities like intangibility and invisibility during a mission where they need to infiltrate a highly - guarded enemy base. His unique perspective as a half - ghost could also offer new strategies to the team.
One possible plot could be that Danny Phantom's ghostly abilities are detected by the Justice League. They initially view him as a threat but then realize he can be an asset. Danny could help them with foes that have intangible or otherworldly powers. For example, against an enemy that can phase through walls or possess people, Danny's experience dealing with ghosts would come in handy.
It could be that the Dark Lord offers Harry something irresistible. Like a way to bring back his parents. Harry, being desperate to have his family back, might be tempted to join the Dark Lord in the fanfiction. After all, the love for his parents was always a strong driving force in his character, and this could be a major turning point that leads him to side with the Dark side.
In a Natsu joins Zeref fanfiction, one possibility is that Natsu could initially be conflicted. He has always seen Zeref as an enemy, but perhaps there's a common goal they discover. For example, they might find out about a greater evil that threatens the entire magical world. Natsu's fiery nature could be used in a new way when combined with Zeref's dark magic. This could lead to a very different power dynamic compared to what we see in the original Fairy Tail story.