Natsu could be influenced by the dark guild's evil ways. He may start using more underhanded tactics in battles instead of his usual straightforward and fair fighting style. For example, he might be forced to use dark magic that corrupts his soul little by little.
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.
She might lose her friends. In the original story, her friends in Fairy Tail are a big part of her life. If she joins a dark guild, they would likely see her as a traitor. For example, Natsu might be very disappointed and try to bring her back to the right side.
The plot could involve Naruto being an outcast in the ninja world after some false accusations. The dark guild offers him a place where he feels accepted. However, the guild's activities are against the values he once held. So he has to decide whether to stay and try to change the guild from within or break away and face the consequences of having associated with them in the first place. It could also lead to some interesting battles where Naruto uses his unique skills against his former comrades who now see him as a threat.
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.
Well, one possible plot could be that Natsu, after some sort of betrayal in Fairy Tail, decides to create his own dark guild. He might gather some disgruntled mages who also feel wronged by the mainstream guilds. Their goal could be to change the magic world's power structure in a more radical way, using darker forms of magic that are usually shunned. For example, they could explore ancient and forbidden magic spells to gain an edge over other guilds.
His character could become more conflicted. He has to balance his old values from Fairy Tail with the new, darker ones of the guild he joined.
Well, in fanfiction where Natsu leaves the guild, he could become a sort of lone wolf. He might travel to far - off lands to discover more about his dragon - slayer powers or his past. This could lead to him meeting new and powerful allies or enemies. Without the support of the guild, he would have to rely solely on his own strength and wits. It could also make him a more serious and hardened character, as he no longer has the safety net of his Fairy Tail family.
It could be the leader of the dark guild. This person would likely have a very different ideology from Naruto's. Maybe the leader believes in using extreme and unethical means to gain power, like sacrificing innocent lives for dark magic. Naruto would constantly clash with this leader as he tries to uphold his own values.
One possibility could be that Natsu is under some sort of dark magic influence. Maybe a powerful enemy has managed to control his mind, making him turn against the guild master. Another reason could be a misunderstanding. If some false information is fed to Natsu about the guild master being a threat to the guild or his friends, his hot - headed nature might lead him to take drastic action without fully understanding the situation.
Well, one possibility could be that Natsu leaves the guild because of a personal mission. Maybe he discovers a dark secret about his past that he believes can only be solved alone, so he leaves Fairy Tail to find out the truth without putting his friends in danger.
In fanfiction, Naruto joining could lead to alternate storylines. Maybe he'd find himself in a modern - day setting instead of the Hidden Leaf Village. He could use his ninja skills in a completely different environment, like a big city, which would be really interesting to see how he adapts.