One possible reason could be a powerful jutsu gone wrong. Maybe a time - related jutsu was misfired and it sent Naruto's body back to a pubescent state. Another reason might be a curse or some sort of magical affliction placed on him by an enemy.
Perhaps it's a consequence of a deal Naruto made with a powerful entity. He might have made a pact in order to gain some great power or save his friends, and part of the deal was to go through puberty again as a test of his will and ability to adapt to new situations.
Well, if Naruto has to go through puberty again in the fanfic, it could make him more self - conscious. He might re - experience the insecurities and awkwardness that come with puberty. This could lead to a more nuanced understanding of his past self and how far he has come in his original growth.
Poison or some sort of harmful jutsu effect. Maybe an enemy uses a special poison or a jutsu that slowly weakens Naruto's body. In the fanfic, this could be a new and unique type of attack that he has not encountered before, and his body is not able to withstand it, resulting in fainting.
It could be that Naruto has an epiphany about love and friendship. He might realize that his love for Sakura was more of an infatuation based on their childhood experiences. As he matures, he understands that true love should be mutual and free. So, he decides to let go of Sakura to find a relationship where his feelings are reciprocated, and also to respect Sakura's own choices.
One reason could be curiosity. Naruto might be curious to see how fans imagine different scenarios in the Naruto Shippuden universe. Maybe he wants to see how others view his friends and his own adventures.
Maybe he got too stressed out from all the responsibility of being a hero. The pressure of protecting the village and his friends could have pushed him to pick up smoking as a way to relieve stress.
Perhaps he thinks fanfic undermines the integrity of the original Naruto story. The official story has a certain narrative and character development, and fanfic can deviate from that significantly. When it comes to his connection with Naruto, any deviation in fanfic might be seen as a negative. For example, if a fanfic changes the way he mentors Naruto, it could be something he wouldn't like.
In a more comical sense, Naruto could be really hungry and he thinks Ino has some delicious food. So he breaks in, not realizing it's inappropriate. But this could then lead to a funny adventure where they end up cooking together or something like that.
In some fanfics, there could be a misunderstanding. Suppose Kushina did something that Naruto misinterpreted as harmful to him or his friends. This misinterpretation could lead to his hatred. For example, if Kushina was involved in a mission that Naruto thought put the village at risk, but in reality, she had no choice.
In fanfics where Naruto attempts suicide, it could be due to extreme loneliness. He has often faced isolation in the original story, and in some fan interpretations, that feeling could be amplified to a point where he sees no way out. Another reason might be failure. If he fails in protecting his friends or achieving his goals in the fanfic's alternate storyline, he could feel so despaired that he contemplates suicide.
One possible reason could be that Naruto has faced too many betrayals. Maybe his friends turned on him in the fanfic, which made him lose faith and stop caring.