Perhaps in the 'naruto is dead fanfiction', his friends like Sasuke might go on a dark path of revenge, blaming themselves or others for Naruto's death. This could lead to a lot of internal conflict within the group of friends.
One possible storyline could be how the Hidden Leaf Village copes with his death. Maybe there are power struggles as different clans vie for leadership in the absence of Naruto's unifying presence.
One possible storyline could be that Naruto died in a great battle against a powerful new enemy. His friends then have to deal with the grief and the power vacuum his death leaves. For example, Sasuke might feel a deep sense of loss and guilt, as Naruto was his closest friend and rival. Another could be that Naruto was assassinated by a hidden organization within the ninja world, which then leads to a mystery that his friends and allies have to solve to bring justice to his death.
One possible storyline could be Francis and Zoey getting separated from the rest of the group during a horde attack. They then have to rely on each other's skills to survive, with Francis using his brute strength and Zoey her sharpshooting. Another could be a story where they discover a hidden safe zone that seems too good to be true and must figure out if it's a trap. Maybe they also find an abandoned research facility that holds the key to a possible cure, and they have to protect it from other survivors who want to use it for their own gain.
One possible storyline could be that Kalawarner somehow ends up in the Naruto universe. She might be confused at first but then use her own skills to help Naruto and his friends in a battle. Maybe she has some unique powers that are useful against a new enemy.
One possible storyline could be that the OC is a new student who quickly befriends Shizuka. They end up having to rely on each other during the zombie apocalypse. For example, the OC might have some unique survival skills like being able to find hidden shelters, and Shizuka uses her medical knowledge to keep them healthy. Together, they form a strong bond and help other survivors as well.
A storyline could involve Naruto using his newfound Nara abilities to solve a mystery in the village. Maybe there's a strange phenomenon that's related to shadow - based jutsu, and Naruto, with his understanding of both Uzumaki and Nara powers, is the only one who can figure it out. He'd have to team up with other characters, and in the process, there would be a lot of character development and interesting interactions.
Another storyline might be that Millet is a secret organization in the Naruto world. Naruto discovers that this organization has been pulling the strings behind some of the conflicts. He has to infiltrate it and expose their true motives. This would be a great opportunity for Naruto to use his stealth and combat skills, as well as his ability to make friends and allies within the organization to bring it down from the inside.
One possible storyline could be that Naruto is chosen as a temporary Kazekage due to a threat that requires his unique skills. He then has to deal with internal conflicts within the Sand village while also facing external enemies. Another could be that there is some kind of prophecy that only Naruto can fulfill as Kazekage to save both Konoha and Suna.
One possible storyline could be Naruto as an elf trying to fit into the ninja world while still having his elf heritage. He might face discrimination from some who don't understand his different nature.
In a Naruto and Derieri fanfiction, a possible storyline could be that Derieri is mistaken for an enemy in the Naruto universe. Naruto, being the one to see her potential for good, tries to convince others that she is not a threat. As they try to clear her name, they uncover a conspiracy that threatens both their worlds. This would involve a lot of mystery - solving and action as they race against time to stop the conspiracy.
In a Naruto fanfiction, Jaune Arc could start his own ninja clan. He could use his knowledge from RWBY to create a new style of combat that combines aura and chakra. Maybe he falls in love with a kunoichi and has to deal with the cultural differences between his world and the Naruto world while also facing off against powerful villains who want to steal his new - found ninja techniques.