Sakura could be a main character. She is a skilled medic - ninja. So, she might be involved in trying to figure out why the flowers are wilting. Maybe she thinks it's related to some new disease in the plant life of the Naruto world and she uses her medical knowledge to investigate.
It might also be a story where the wilting flowers are a result of some dark magic or a curse in the Naruto world. Naruto has to go on a quest to find the source of this curse and break it to save the flowers. He could meet new characters or face new enemies during this quest.
Sakura could be a great main character. You could show her growth during the bell test, not just as a ninja in terms of skills, but also in her self - confidence. Maybe she has to take the lead when Naruto and Sasuke are incapacitated for some reason.
Sasuke could be a great choice. He has that brooding, anti - hero vibe that could fit well in the criminal underworld. Maybe he gets drawn into the crime boss's schemes because he thinks it's a way to gain more power to achieve his own goals.
Hinata could be an idol trainee. She is shy at first but as she trains, she becomes more confident. Naruto could be her biggest supporter, and their relationship could develop further as they both pursue their dreams in the idol and ninja worlds respectively.
There could be members of the Gremory family. For example, Rias Gremory might be a key character. She could be one of those who initially neglect Naruto but later come to realize his potential. Another character could be Issei Hyodo, who might be in a position where he has to choose between the traditional Gremory way and Naruto's different approach.
Kakashi could also be a main character. He has lost many people close to him, like his father, Obito, and Rin. Facing the death goddess, he could be in a moral dilemma. He might be tempted to use her power to change the past, but also realizes the consequences that could come with meddling with death. His internal struggle could be a central part of the fanfiction.
It could be Sakura. In the original Naruto series, she had feelings for Sasuke for a long time. But in this fanfiction, she could shift her attention to Naruto and be the one who wants him to be hers. Maybe after seeing Naruto's selfless acts and his growth, she realizes that he's the one she should be with.
A young African girl could be a main character. She might take Naruto under her wing, showing him around the village and teaching him about African traditions like dancing and making handicrafts. Also, a powerful African sorcerer could be in the story. He might view Naruto as an intruder at first but then realizes Naruto's good intentions and teams up with him to fight against a common enemy that threatens both their worlds.
There could be a new character introduced, perhaps an old hermit who is an expert in sealing. This character could have some hidden motives, like using Naruto's newfound skills for his own gain at first but then eventually becoming a true ally after seeing Naruto's pure intentions with the power of sealing.
It's hard to say without reading the fanfic, but it could be characters like Sasuke. Since Sasuke is Naruto's rival, he might be involved, either competing with Naruto over the use of the Raijin no Ken or joining forces with him. Kakashi is also a likely character to be in it as he has knowledge about many ninja techniques and could play a role in guiding Naruto in using the weapon.