Initially, the relationship could be tense. Naruto is used to his own way of life in the ninja village, and Sekirei has its own set of rules. But when the little sister enters the picture, things change. They both realize that they need to cooperate for her well - being. Naruto could be a bit overprotective, which Sekirei might find endearing. Sekirei, on the other hand, could bring a sense of calm and elegance to the group. As the little sister grows, she would start to mediate between them when they have differences, making their relationship more harmonious and like a real family.
One possible plot could be that the little sister has a special power. For Naruto, she might be a ninja with unique jutsu. In the Sekirei world, she could be a Sekirei with a new type of ability. Maybe she gets caught in the middle of a conflict between the two worlds, and Naruto and the Sekirei have to work together to protect her.
It might not be extremely popular. While both Naruto and Sekirei have their own large fanbases, combining them in a fanfiction in this way is a rather niche idea. Many fans of each series are more focused on the original storylines, characters, and lore of their respective shows. However, there are always some fans who enjoy exploring crossovers and unique interpretations, so it could have a small following among those who like to think outside the box in fanfiction.
A Naruto and Sekirei fanfiction crossover can be really interesting. In such a story, the different power systems from both Naruto and Sekirei universes could be combined in unique ways. For example, the ninjutsu from Naruto might interact with the Sekirei's special abilities. Characters from both series could also form unexpected alliances or rivalries. Maybe Naruto characters could learn about the Sekirei Plan and get involved, or Sekirei could be introduced to the concept of chakra.
Naruto's chakra could potentially enhance the Sekirei abilities. For instance, if a Sekirei has a power related to speed, Naruto could use his chakra to further boost that speed. His Rasengan could also be modified when combined with a Sekirei's power. Maybe it could take on new forms or have additional effects.
The storylines could be blended by having a shared goal. Suppose there is a threat that endangers both the Naruto world and the Sekirei world. It could be a new, powerful and evil force. Characters from both series would then have to work together to defeat this threat. Along the way, they would learn about each other's worlds, powers, and cultures. For instance, Naruto characters could teach Sekirei about teamwork in the context of a ninja squad, while Sekirei could show Naruto characters their unique way of bonding with their Ashikabi.
In this type of fanfiction, it could be that Naruto enters the Sekirei world during one of his training missions gone wrong. He is neglected by the Ashikabi (the Sekirei masters) at first because he doesn't seem to have any Sekirei - like powers. However, Naruto's strong will and determination attract a Sekirei who is also different from the others. They start to train together, Naruto teaching the Sekirei about ninja values like loyalty and perseverance. As they progress, they start to change the perception of what it means to be strong in the Sekirei world, and Naruto becomes an important figure despite the initial neglect.
Well, in fanfiction, anything is possible. Maybe Naruto gets transported to the Sekirei world through some sort of magic or a strange portal. This could be the start of his journey to become a Sekirei. It could also be due to a curse or a wish gone wrong that transforms him into a Sekirei - like form.
A common theme is power combination. Writers often explore how Naruto's powers, like his Rasengan or Shadow Clone Jutsu, can be combined with the Sekirei's powers. Another theme is the clash of cultures, as the ninja world of Naruto and the modern - yet unique - world of Sekirei collide.
Well, it could be that in this fanfiction, Naruto is given a mission that goes against the interests of the Sekirei. He might have to choose between his loyalty to his original world and the new relationships he has formed with the Sekirei. If he chooses his old world, the Sekirei could see it as a betrayal.