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.
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.
One possible storyline could be Naruto struggling to balance his ninja duties with raising his child alone. Maybe he has to take the kid on missions sometimes, teaching the little one about the ninja world along the way. Another could be Naruto dealing with the judgment of the village as a single father, showing how he overcomes that and still raises a strong and kind - hearted child.
Well, in Naruto fanfiction, if there's a neglected baby, it might be that the baby is the offspring of a missing - nin. The village, fearing the baby could grow up to be like its parent, neglects it. Maybe the baby has a chakra nature that is considered 'cursed' in the Naruto world, like some form of dark chakra. As a result, the people around avoid the baby, leaving it to fend for itself in a cruel environment.
Perhaps in a fanfiction, Naruto discovers some dark secrets about his parents that shatter his world view and send him into a depressive state. Temari, being a friend, comes to Konoha on a diplomatic mission and finds Naruto in this state. She tries to help him by sharing her own experiences of dealing with difficult family situations. However, the more she tries, the more she realizes how deep Naruto's pain is and she herself starts to feel a bit depressed due to her inability to fully help him.
Well, in some fanfictions, Itachi might seem to be cheating on Naruto in the sense that he's forming closer alliances with other characters for strategic purposes. For example, he could be getting involved with another ninja clan to gain information or resources for the greater good, but Naruto misinterprets his actions as being unfaithful in their friendship.
Another idea is that Naruto, while on a mission, stumbles upon a portal that leads him to the world of the Thundercats 2011. There, he meets Cheetara and they form an alliance. They could face off against common enemies like powerful villains from both universes who are trying to take over both worlds.