A new character could be created as the main villain. Maybe a rogue ANBU agent who was once a friend of Naruto and Sasuke but has been corrupted by power. This character would know all the ins and outs of the ANBU, making it very difficult for Naruto and Sasuke to stop him as he tries to take over the ninja villages using the secrets he learned while in the ANBU.
One possible scenario in such a fanfiction could be Naruto as Hokage having to deal with political situations in the village while Sasuke, as an Anbu, is sent on dangerous covert missions. Naruto might rely on Sasuke's intelligence and combat skills from his Anbu work to protect the village from external threats. They could also have some internal conflicts due to their different roles and the secrecy associated with Sasuke's Anbu work.
A really interesting fanfiction idea could be that Sasuke in the Anbu discovers a conspiracy within the village that even Naruto as Hokage is unaware of. Sasuke then has to decide whether to go to Naruto directly or investigate further on his own. This would create a lot of tension and drama, as Sasuke's loyalty to the village and his relationship with Naruto are both at stake.
It could be Orochimaru. He has always been interested in Sasuke and might target ANBU Team 7 to get to him. Orochimaru's experiments and his desire for power make him a formidable and menacing villain. He could also be using some new jutsu or have created more powerful minions to fight against Team 7.
Perhaps a powerful ninja from another village who has a vendetta against Konoha and the ANBU. They see the ANBU's connection with Naruto as a threat and use their knowledge of the lemon fanfiction element in some way. For example, they might create clones that are disguised as lemon - scented ANBU members to infiltrate Konoha and cause chaos.
One idea for the main plot is that a group of rogue ninjas has developed a new and dangerous jutsu that can disrupt the balance of power in the ninja world. Naruto, in his role as Hokage, decides to take action. Sasuke, as an Anbu, is sent to infiltrate the group. As Sasuke gets closer to the truth, he finds that the leader of the rogue ninjas has a personal vendetta against Naruto. This forces Sasuke to race against time to stop the jutsu and protect Naruto and the village. Along the way, Sasuke also has to come to terms with his own past actions and how they might affect the current situation.
Another theme is the exploration of the ANBU world itself. These fanfictions often describe the dark and dangerous nature of the ANBU, the strict training, and the complex hierarchy. Sasuke's experience in this world is then contrasted with his relationship with Naruto, who represents a more positive and hopeful side of the Naruto universe.
Their relationship would be one of mutual respect. Naruto, as Hokage, would trust Sasuke's abilities as an Anbu member. Sasuke, on the other hand, would respect Naruto's leadership. They would be comrades again, but with a new dynamic due to their different positions in the village.
Another reason might be related to their different ideologies within the ANBU. Naruto may have believed in a more collaborative and friendly approach within the organization, while Sasuke might have been more focused on individual achievement and power. This fundamental difference could lead to Naruto hating Sasuke in the fanfiction.
It could be Orochimaru. He might be jealous of their new merged power and see it as a threat. So, he tries to find a way to either steal it or destroy them.
It could be an unknown, ancient evil that has been awakened. This villain might have powers far beyond what Naruto and Sasuke have faced before. Maybe it's an entity from a forgotten era that was sealed away long ago and now has broken free.