The storylines can differ in many ways. In the original Naruto series, the focus is mainly on the ninja world, its politics, and the battle against evil forces like Akatsuki. In a crossover, new threats could emerge that are related to the Sekirei world. For example, a group that wants to use both ninja and Sekirei powers for their own malicious ends. Also, the relationships in a crossover can be different. Instead of just the typical Naruto friendships and rivalries, there could be romantic relationships between Naruto characters and Sekirei, which is not a part of the original Naruto plot.
In a Naruto and Sekirei crossover fanfiction, the storylines can deviate from the originals by introducing new power dynamics. The original Naruto has a fairly established power hierarchy based on chakra levels and ninja skills. But when Sekirei powers are introduced, it can completely disrupt that. A low - level ninja in Naruto might suddenly become very powerful with the addition of Sekirei powers. Also, the narrative focus can change. The original Sekirei focuses on the Sekirei Plan and the relationships between Ashikabi and Sekirei. In a crossover, this focus could shift to something more inclusive, like saving both the ninja world and the Sekirei world from a common threat that neither could face alone. This would create a whole new set of storylines that are different from what we see in the individual series.