One reason could be the trauma he experienced during the Wave mission. He might have seen the darker side of the ninja world, like the cruelty of Zabuza and Haku's situation. This could have made him more guarded and seemingly cold as he realizes the harsh reality.
In the fanfiction, perhaps Naruto was betrayed by someone in Wave. Maybe a villager he thought he could trust turned on him. This act of betrayal could have led him to close off his emotions and become cold to protect himself from further hurt.
Another possibility is that Naruto witnessed the powerlessness he felt during the Wave events. He couldn't save everyone, and this feeling of inadequacy might have changed his once - warm personality. He might think that being cold and more calculating would make him a stronger ninja in the future.
One possible reason could be a sense of being undervalued. Maybe he felt that his teammates didn't fully appreciate his efforts during the Wave mission. For example, if Sasuke got most of the credit, Naruto might feel pushed aside.
Well, one reason could be that he's kidnapped by a secret organization. They might see his potential and want to use him for their own evil plans.
Another reason could be the influence of a powerful and dark entity. If Naruto is somehow possessed or influenced by a dark chakra or a malevolent spirit, it might change his personality completely. He could start to push away people who care about him because the entity wants him to isolate himself and be more vulnerable to its control.
It could be due to a new jutsu he's trying to master that has some side effects on his emotions. Maybe it's a powerful ice - based jutsu that's making him cold in nature as well.
Perhaps in this fanfiction, Naruto and his friends go back to the Wave Country for a follow - up mission. This time, they discover a new threat that is related to the power struggle they witnessed during the first mission. The group has to use their improved skills and teamwork to face this threat and protect the people of Wave.
In some fanfictions, it could be due to a powerful emotional shock. Maybe seeing a friend in great danger at Wave, like Sasuke almost dying, could trigger an unexpected connection to the Sharingan. Since Naruto has a strong bond with Sasuke, this extreme situation might force his latent Uchiha - like powers (in the context of the fanfic) to surface, awakening the Sharingan.
It could be related to some sort of external influence, like a curse or a dark chakra that has infected him. This could be slowly changing his personality from the warm - hearted Naruto we know to a cold - hearted version. For example, if there was a powerful enemy who placed a curse on him that targeted his emotions.
It could be due to a personal loss that has hit him really hard. Maybe he lost someone very close to him, like Jiraiya all over again, but this time it has broken him in a way that he shuts everyone out. He might also be under the influence of a new power that he doesn't fully understand yet, and this power is affecting his emotions, making him cold as a side - effect until he learns to control it.
He may start to distance himself from his friends. Instead of being the overly friendly Naruto, he becomes more reserved. For example, he might not be as quick to join in on group activities or conversations.
The main antagonist could also be a corrupt official within the Wave Country itself. After the events of the first mission, this official could have risen to power and now has plans to use his position to gain more control, even if it means going against Konoha. He could be secretly working with other villains or using his own resources to create problems for Naruto and his friends.