Well, without more context, 'her' could be any number of characters. It might be a new character created for the fanfiction. Natsu might want her to join Fairy Tail because he sees potential in her magic abilities. Fairy Tail is all about accepting people with different powers and making them part of the family.
Perhaps there's an antagonist who doesn't want 'her' to join Fairy Tail. This creates a conflict. Natsu has to fight against this antagonist to protect 'her' and ensure she can join the guild. Along the way, 'her' might start to develop feelings for Natsu as she sees how much he cares about her joining.
If Natsu and Zeref join Fairy Tail in fanfiction, it would change the dynamic of the guild completely. The other members would have mixed reactions. Some might be distrustful of Zeref due to his past actions. However, as time passes, they could see the good in him. Natsu and Zeref together could attract a lot of attention from outside forces. Enemies might target Fairy Tail more because of their combined power. But also, they could inspire the guild to become even stronger, with everyone striving to keep up with their new powerful comrades.
One reason could be that the author wants to create an alternate universe where Natsu has a different path. Maybe in this fanfiction, he has a prior commitment to another guild or group that prevents him from joining Fairy Tail.
In this fanfiction, the story might take a darker turn. Natsu is like the heart and soul of Fairy Tail in many ways. Without him, there could be a sense of gloom in the guild. However, this could also be a catalyst for change. Characters like Wendy could step up more. She might start to explore and master her dragon slayer magic in ways she hadn't before. And the relationships between the characters would shift, perhaps becoming more complex as they deal with the absence of Natsu.
Perhaps a plotline where an outside force tries to manipulate Natsu and Zeref against each other while they are in Fairy Tail. This could lead to a lot of internal conflict within the guild as members take sides. But in the end, through the power of friendship and the values of Fairy Tail, they see through the ruse and become stronger together, uniting the guild even more firmly.
One possible reason could be a misunderstanding. Maybe Erza misinterprets Natsu's actions as being reckless and endangering the guild, so she takes harsh measures to 'teach him a lesson'.
The story could also revolve around how the guild members' relationships change. For instance, Happy might not be as cheerful without Natsu around. And the guild as a whole might become more united in trying to find a replacement for Natsu or trying to figure out how to move forward without him. They could start to explore different parts of the magical world to find new allies or magic that can help them in their battles.
One possible reason could be for a practical joke. Lucy might be in a playful mood and think it would be funny to tie Natsu up and see his reaction. Another reason could be for his own safety. Maybe Natsu was about to rush into a dangerous situation without thinking, and Lucy tied him up to stop him. It could also be part of a training exercise. If Natsu needs to learn how to break free from restraints in combat situations, Lucy could be helping him by tying him up and making him figure out how to escape.
One popular 'End Join Fairy Tail' fanfiction might be 'The New Adventure'. It often features new characters joining the Fairy Tail guild and going on unique quests. Another could be 'End Join: The Power Within' which focuses on the development of the joined characters' powers within the Fairy Tail universe.
In a fanfiction, there could be a situation where Lucy is forced to side with a group that Natsu is against. This would make Natsu see her as an enemy. Or perhaps there is a prophecy that Lucy is involved in that Natsu misinterprets as something bad. He might think she is a threat to the guild or his friends. Also, if there is a love triangle situation where Lucy chooses someone else over Natsu in a way that really hurts his feelings, that could be a reason for him to start hating her.