One idea could be to create a story where the Akatsuki members from Naruto end up in the DxD universe and have to deal with the devils, angels and fallen angels. They might use their unique ninja skills in battles against the supernatural beings in DxD.
You could also write a fanfiction where the power systems of both Akatsuki and DxD are combined. Imagine a character who has both the Sharingan from Akatsuki - related powers and the Boosted Gear from DxD. This would create a really unique and powerful character, and the story could explore how they rise to power in this combined universe.
You could write a fanfiction where the Akatsuki are summoned to the Highschool DxD world by a powerful magic user. They then get involved in the power struggles between the different factions. Maybe they side with the devils at first, but then realize that the angels also have some good points. The interactions between the Akatsuki members and the characters from Highschool DxD would be really interesting to explore, like how Sasori might react to the technology in the Highschool DxD world compared to his puppet - making skills.
A plot could revolve around a mystery in Akatsuki High School. There could be a series of strange events happening, like students disappearing or strange symbols appearing. The DxD characters would then have to use their skills and knowledge to solve the mystery, which could lead to uncovering a dark secret about the school's past.
A fanfiction could also explore a world where the Akatsuki and RWBY teams are merged into one super - team. The different fighting styles and abilities would make for really exciting battles. Characters like Itachi with his Sharingan and Blake with her semblance could combine their skills in stealth and combat to outwit their enemies.
You could make an OC who is a healer by nature but is forced to join the Akatsuki. This OC could then struggle with the group's more violent and unethical actions while still trying to use their healing skills to keep the members alive, leading to many internal conflicts within the story.
Well, a plot could be Naruto is on a mission to infiltrate the Akatsuki, but he starts to understand their motives which are not entirely evil in some aspects. For example, some members might have joined because they were persecuted by their own villages. Naruto could then try to find a middle ground between the Akatsuki and Konoha, to create a sort of peace deal. This would be a really different take on the Naruto - Akatsuki relationship compared to the original story.
You could write a fanfiction where the Akatsuki organization from Naruto has some sort of connection to the events in Akatsuki no Yona. For instance, the Akatsuki are after a powerful artifact in Yona's world that they believe will give them ultimate power in their own world. Yona and her friends then have to stop them while also dealing with their own internal political and social issues in their kingdom.
One idea could be Sakura infiltrating the Akatsuki to gather information for the Hidden Leaf. She might start to understand the motives of some Akatsuki members and question her own village's view of them.
Another interesting crossover could be with 'Sailor Moon'. The Sailor Scouts could join forces with Yona's gang. Yona could learn about the power of friendship and magic from the Scouts, and they could work together to protect both their worlds from a new, menacing threat.
One idea could be Naruto joining the Akatsuki but secretly working to reform it from within. He could try to change the views of members like Hidan and Kakuzu by showing them a different way of life. Another plot could involve Naruto being sent on a mission by the Akatsuki that makes him question his loyalty to the group. For example, if the mission is to harm innocent people, Naruto would have to find a way to complete the mission without actually causing harm.
One idea could be that a Naruto character gets accidentally transported into the Akatsuki's hideout. They then have to figure out how to get back while avoiding being captured or worse. Another could be a scenario where an Akatsuki member has a change of heart due to an encounter with Naruto and his friends, and decides to help them instead. Maybe a joint mission where Naruto and the Akatsuki have to team up against a greater threat that endangers both their worlds.