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.
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.
Lucy's celestial magic could be a very unique addition to Phantom Lord. They might not have anyone with such magic before. So, she could use her keys to gain an advantage in battles or for other strategic purposes within the guild. For instance, she could use her Aquarius key to control water sources during a fight or her Taurus key for brute strength when needed.
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.
He might lose his friends at Fairy Tail. Since Fairy Tail is all about friendship and light, joining a dark guild would put him at odds with his former comrades.
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.
Perhaps an old enemy of Fairy Tail who sees Natsu as a new threat. They might target Natsu specifically to prevent him from strengthening the guild. This antagonist could have a long - standing grudge against Fairy Tail and see Natsu as the new hope for the guild, so they try to eliminate him before he can fully join.