She might start by having Lucy grow disillusioned with the normal guilds. Maybe she's been mistreated or feels restricted. So, she decides to gather like - minded mages who also have issues with the existing guild system. They could start small, doing jobs that are a bit on the edge of legality. As they gain power and members, they face opposition from the regular guilds. This could lead to epic battles and a lot of character development for Lucy as she struggles between her old ideals and the new, darker path she's chosen.
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 center around Lucy's transformation as she does the guild paperwork. At first, she might be frustrated and overwhelmed, but as she delves deeper, she starts to understand the importance of it for the guild's functioning. She could also find some hidden secrets or messages in the paperwork that lead to an adventure.
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.
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.
The plot could revolve around a new Dark Guild that is formed specifically to take over both the Naruto and Fairy Tail universes. They start by stealing important artifacts from both worlds. Naruto and a team of Fairy Tail's strongest mages are brought together by a mysterious force to stop this new threat. As they investigate the Dark Guild, they discover that the guild's leader has a personal vendetta against both Naruto and Fairy Tail. This vendetta drives his actions and makes him a formidable foe. In the end, through teamwork, strategy, and the unique powers of both Naruto and Fairy Tail, they are able to defeat the Dark Guild and restore peace to both universes.
The Magic Council would be a major opponent. They are in charge of maintaining order in the magical world. A dark guild led by Lucy would be seen as a direct challenge to their authority. Also, any heroes or powerful mages who uphold the values of the regular guilds would oppose her. They would not want a dark guild to gain power and influence, as it could lead to chaos in the world of magic.
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.
Her Celestial Spirit powers could be misused. Instead of using her spirits for good, like in Fairy Tail, she might be made to use them to intimidate or harm others. The spirits might also be reluctant to follow her commands if they sense she is on the wrong path.
In this fanfiction, Naruto could build a guild to train the next generation of ninjas in a new way. He realizes that the traditional village - based training has some limitations. So, he creates a guild where the focus is on individual growth as well as teamwork across different bloodlines and abilities. The guild might also attract some former villains who want to reform and contribute to a new ninja society.
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.