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.
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.
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 idea could be that Kirby accidentally gets transported to Bayonetta's world. Kirby's cute and innocent nature would contrast greatly with Bayonetta's more sultry and powerful demeanor. Maybe Kirby could mistake some of Bayonetta's enemies for his own and start gobbling them up, causing confusion but also helping Bayonetta in the process.
The most interesting element is the combination of different power systems. Naruto has his chakra - based ninja abilities like rasengan, while Bayonetta has her guns and witch powers. When these are combined in a fanfiction, it creates really exciting fight scenes. For example, imagine Naruto using his shadow clones while Bayonetta is summoning demons and they are fighting a common foe together.
One interesting crossover could be the combination of Naruto's ninja skills with Bayonetta's witch powers. For example, Naruto could use his shadow clones in a fight while Bayonetta uses her summoned demons. They might team up to face a powerful enemy that threatens both their worlds. Maybe a villain from the Naruto universe that has some connection to the forces of evil in Bayonetta's world.
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.
The OC could be a journalist who is trying to uncover the secrets of the world of Bayonetta. Bayonetta at first tries to avoid the OC but eventually they form an alliance as the OC's skills prove useful in their battles and investigations.
In a fanfic, Madama Butterfly could lose her memory. Bayonetta then has to help her regain it while also protecting her from enemies who see this as an opportunity to attack. Bayonetta could show Madama Butterfly old memories through their shared magic, and in the process, they both learn more about each other and their own powers.
Another theme is the clash of cultures. Bayonetta comes from a very different world compared to Naruto's. So in fanfiction, there can be a lot of exploration about how their two worlds' cultures interact. This could involve things like how Bayonetta reacts to the ninja villages, or how Naruto and his friends view Bayonetta's more modern - looking (compared to their world) appearance and technology.