A really interesting plot could be a time - travel based one. Bayonetta somehow travels back in time to the era of the Ninja in the Naruto world. She has to adapt to the different culture and fighting styles. Naruto and his team help her out, and in return, she teaches them some unique combat moves. They end up changing the future of both worlds in some way by working together against a threat that was supposed to destroy both worlds in the future.
Perhaps there could be a plot where a villain from the Naruto universe uses Bayonetta's world as a hiding place. Naruto and Bayonetta meet while both are on the hunt for this villain. Bayonetta is initially suspicious of Naruto but soon realizes his good intentions. As they work together, Naruto's ability to sense danger with his ninja skills and Bayonetta's combat prowess make them a formidable duo.
A plot might involve Naruto being sent to Bayonetta's world. He'd be out of his element, but his determination would shine through. Bayonetta could mistake him for a strange demon at first. However, they soon realize they can help each other. Naruto's chakra could interact in unexpected ways with Bayonetta's magic. Together, they could face off against Bayonetta's foes, like the angels, with Naruto's Rasengan combined with Bayonetta's Witch Time abilities making for some epic battles.
One idea could be a crossover where Naruto's world is invaded by some of Bayonetta's demonic foes. Naruto and his friends have to learn new ways to fight, perhaps using some of Bayonetta's combat techniques. Another could be a story where Bayonetta ends up in the Naruto universe and teams up with Naruto to take on a common enemy that threatens both their worlds. She might introduce her unique style of magic and combat to the shinobi world.
Another idea is that Bayonetta somehow ends up in the Naruto universe. She might be mistaken for a powerful ninja at first. Then she could start teaching some of the ninja new combat techniques inspired by her own moves, while also learning about chakra and how it differs from her own power source.
You could have an OC that is a young witch who idolizes Bayonetta. She tries to copy Bayonetta's style and fighting techniques but often fails in a comical way at first. As the story progresses, she discovers her own unique way of being a witch. Or an OC who is a cursed object collector. This OC comes across Bayonetta when investigating a powerful cursed object and they end up working together to either destroy or control the object's power.
One interesting plot idea could be a crossover where Naruto's senjutsu abilities are combined with another universe's magic system. For example, if he were to cross over into the Harry Potter universe, he could use senjutsu to enhance his magic or even teach the wizards about chakra. Another idea is a crossover with the Dragon Ball universe, where Naruto's senjutsu clashes with the ki energy of the Saiyans. Maybe he has to use senjutsu to face off against a powerful Saiyan who has come to the Naruto world. Or a crossover with the Bleach universe, and Naruto uses senjutsu to interact with the spiritual energy there, perhaps even helping Ichigo in a battle against a powerful Hollow by using his unique senjutsu skills.
One plot idea could be that Naruto characters end up in Ikebukuro. For example, Naruto himself could be searching for a new type of ninja tool that he heard can only be found in Ikebukuro. Meanwhile, the gangs in Durarara start to notice this strange, orange - clad boy with strange powers. Another idea is a character swap where some of the Durarara characters gain ninja abilities and get involved in Naruto - style battles in their own world. Maybe Celty could use her shadow powers in a more ninja - like way, like stealth and quick attacks.
One idea could be that Naruto characters are transported into the Splatoon world. They might initially be confused by the ink-based battles and the unique species. For example, Naruto could mistake an Inkling for a strange ninja from another land and challenge them to a friendly spar, only to find out about the ink shooting mechanism. Another plot could involve the Akatsuki from Naruto trying to steal the valuable ink resources in the Splatoon world for their own purposes. They would face off against the Splatoon heroes who are determined to protect their world's resources.
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.