One idea could be that Naruto is bitten by a werewolf during a mission in a hidden forest. He then has to struggle with his new werewolf nature while still trying to protect the village. Another plot could involve a werewolf clan that has a prophecy about Naruto and they either try to help or hinder him depending on how they interpret it. A third idea is that some of Naruto's friends also get turned into werewolves and they have to find a cure together.
Well, a really cool plot for a Naruto werewolf crossover fanfiction could be that there's a secret werewolf village within the Naruto world. Naruto discovers it by accident. The werewolves there have a unique chakra that Naruto is intrigued by. He tries to learn from them to get stronger. Meanwhile, some of the werewolf elders see Naruto as a threat to their way of life because of his popularity and power. So, there's a conflict between Naruto and the werewolf village that he has to resolve, all while dealing with his own growth as a ninja and now, a part - werewolf.
A plot could involve a werewolf being sent to the 'familier of zero' universe. The werewolf's abilities would be a mystery and source of both fear and fascination. They could end up being hunted or befriended depending on how the story unfolds. It could also lead to a discovery of a common enemy between the two universes.
One idea could be that Naruto and Hinata are part of a werewolf clan in a hidden village. They have to protect their clan from hunters who are after the werewolves' special powers. Naruto, with his usual determination, tries to find a way to make peace between the two groups while Hinata supports him and also uses her gentle yet strong skills to fend off any immediate threats.
One idea could be that the female werewolf is from a hidden tribe in the Naruto world. Naruto stumbles upon her while on a mission in a forest. She initially sees him as a threat but as they interact more, they find common ground in their sense of loyalty to their respective groups. They could team up to fight a common enemy, like rogue ninjas who are hunting the werewolf tribe for their special abilities.
One idea could be that the hybrid character has the speed and agility of a werewolf and the alluring charm and immortality of a vampire. They could be an outcast in both the ninja world and the supernatural world, trying to find their place. Maybe they use their unique abilities to protect the Hidden Leaf from threats that neither Naruto nor the normal shinobi can handle.
One plot idea could be that the female werewolf is from a hidden werewolf clan in the Naruto world. She meets Naruto during one of his missions in a forest. Naruto, being his curious self, is intrigued by her rather than afraid. They form an unlikely alliance to protect the forest from a common enemy, like a group of rogue ninjas who want to cut down the sacred trees there.
One plot idea could be that a werewolf plague spreads in the Naruto world and Tsunade has to find a cure. Since she's a master of medical ninjutsu, she's the best hope. Along the way, she might encounter werewolves with unique abilities that are different from the normal Naruto - style jutsu.
A cool plot could be that there's a tournament across different anime worlds, and Inuyasha and Naruto are chosen to represent their respective worlds. Along the way, they discover similarities in their pasts, like both having some form of demon - related heritage (Naruto with the Nine - Tails and Inuyasha being a half - demon). They also exchange combat techniques. Naruto teaches Inuyasha how to better use chakra control in his attacks, and Inuyasha shows Naruto some unique sword - fighting skills.
One interesting plot idea could be that Kaguya is reborn in the modern Naruto world. She has no memories of her past at first. Naruto discovers her and senses a strange power within her. As she starts to regain her memories, she struggles between her old self and the new world she's in. Naruto has to decide whether to trust her or not.
Perhaps the nine - tailed fox in Naruto and the Avatar state could have some sort of connection. In the fanfiction, the two powers could interact in unexpected ways. For example, when Naruto enters his nine - tailed fox mode, Aang's Avatar state could be affected, or vice versa. They might have to learn to control these interactions to save both their worlds from a dark force that wants to use this power connection for evil.
One idea could be that Naruto gets a gamer power that allows him to level up his ninja skills like in a game. For example, he can see his progress in learning new jutsus as leveling up. Another could be a crossover with a popular game world where Naruto has to fight game bosses using his ninja abilities.