A theme that pops up a lot is the search for identity. In Naruto, many characters struggle with their identity as ninjas, and in Cowboy Bebop, the characters are often on a journey to find themselves. When combined in fanfiction, it creates an interesting exploration of how they can help or hinder each other in this search. Also, the theme of friendship across different worlds is quite common. Characters from Naruto and Cowboy Bebop form unexpected bonds in these fanfictions.
The concept of power and how it's perceived in both universes is a frequent theme. Naruto has its chakra - based powers, while Cowboy Bebop has different forms of combat skills and technology. Fanfiction writers often play with how these powers interact. Additionally, the theme of the loner vs. the community is explored. Cowboy Bebop characters are often loners, while Naruto is all about the ninja village community. Fanfics may show how these two ideas can coexist or conflict when the characters meet.