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.
A possible plot is that Naruto is captured by the Akatsuki and instead of being killed, they decide to brainwash him into becoming one of their most powerful members. But Naruto's inner strength starts to break through the brainwashing, and he has to fight against his new 'Akatsuki self' while also dealing with the other members who don't trust him. Or perhaps Naruto joins the Akatsuki to find out more about his parents, as he suspects they have some connection to the organization.