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.
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.
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.
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.
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.
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.
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.
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.
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.