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.
A cool concept for a Naruto Akatsuki crossover fanfiction could be that there is a new enemy that targets both the Leaf Village and the Akatsuki. This forces them to form an uneasy alliance. Naruto, being the main character, could be the bridge between the two groups. He would have to deal with the distrust from both sides while trying to figure out the motives of this new enemy. The Akatsuki members might also start to see the value in the Leaf Village's way of life through Naruto's actions and ideals.
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.
A great plot idea is to cross Akatsuki with the world of Fairy Tail. The Akatsuki members could be seen as dark guildsmen. They might try to steal Fairy Tail's magic or fight against the guild's most powerful wizards. Their abilities in the Akatsuki world would be a new and dangerous threat in the Fairy Tail universe. This would create a lot of exciting battles and character interactions.
Well, you could do an Akatsuki crossover fanfic with the world of 'One Piece'. Picture the Akatsuki sailing the Grand Line, having to deal with pirates and the Marines. They might be interested in the Devil Fruits for their own purposes. Or you could cross them with characters from 'Fullmetal Alchemist'. The Akatsuki could be intrigued by the concept of alchemy and try to use it for their plans. Also, consider a crossover with 'Attack on Titan'. The Akatsuki facing the Titans would be quite a sight, and they might find new ways to use their powers in that world.
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 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 Naruto joining the Akatsuki for a secret mission to infiltrate a greater evil organization. He has to hide his true intentions from the Akatsuki members while also trying to understand their motives better.
One plot idea could be Hinata getting caught in the middle of a conflict between Naruto and the Akatsuki. Maybe she tries to use her Byakugan to spy on the Akatsuki for Naruto but gets discovered. This could lead to a tense situation where Naruto has to rescue her.
One idea could be that some members of the Akatsuki start to question their mission after getting to know Naruto better. For example, Itachi might secretly help Naruto in his fight against the Akatsuki while still pretending to be on their side. This would add a lot of mystery and tension to the story.
A possible plot for Naruto Akatsuki Family Fanfiction is the Akatsuki members raising a child together. This child could be a powerful being that they found or created. They would have to teach the child their ways, and in the process, the Akatsuki members might change themselves. For instance, Hidan might become more patient while teaching the child about their beliefs, and Kakuzu might learn to be more giving when it comes to providing for the child's needs.