Yugao Uzuki could also be the main character. She's an ANBU and has her own story. Maybe she gets disillusioned with the way Konoha is handling things, like the treatment of certain ninja clans or the way missions are being assigned. She decides to leave and becomes a rogue ninja, but on her journey, she discovers new powers or allies that change her perspective on the ninja world.
It could be Kakashi. He has a complex past and has been part of the ANBU. Given his experiences, he might have a reason to leave Konoha. Maybe he discovers something about the Sharingan or the Uchiha massacre that makes him question the village's integrity. He's a popular and well - developed character, so a story about him leaving as an ANBU would be interesting.
Perhaps the ANBU has a personal vendetta against someone in Konoha who is too powerful to take on while remaining in the village. Leaving Konoha gives them the freedom to train and gather allies to come back and face their enemy. They might leave secretly, under the guise of a mission, and start building their strength in the outside world, all while Konoha is left in the dark about their true intentions.
It could be a rogue Anbu member. This person might be jealous of Naruto's power and popularity within the Anbu. So, they spread false rumors about Naruto which lead to his decision to leave the village. This antagonist would then try to further harm Naruto while he's outside the village, using their own Anbu skills against him.
In some fanfictions, Naruto might leave the Anbu due to internal conflicts within the organization. There could be corruption or power struggles. Naruto, being the idealistic character he is, would not want to be part of such a messed - up system. He might have discovered some dark secrets about the Anbu that made him decide it was not the place for him.
Kakashi could be a great main character as an ANBU commander. He has the skills, experience, and the mysterious allure that suits the role. He's known for his combat prowess and his ability to think on his feet, which are essential for an ANBU commander.
It could be Kakashi. He has a lot of experience and a mysterious past that would fit well with the Anbu Black Ops setting. His Sharingan would give him an edge in their dangerous missions.
Madara Uchiha could also be the main character in this type of fanfiction. Although in the original story his actions are mostly related to his grand plans for the Ninja world, in a fanfiction, it could be explored what would happen if he decided to leave Konoha specifically because of his Rinnegan and the power it holds.
There's also a chance that the main character could be a completely new character from a minor clan in the Naruto universe. This character could have some hidden bloodline limit that makes them a prodigy in the ANBU. They might start as an underdog but quickly rise through the ranks due to their exceptional skills and intelligence.
One option for the main antagonist could be a secret organization that has infiltrated Konoha. They target the Anbu prodigy because they fear the prodigy's abilities could expose their existence and plans. This organization might have members with unique and dangerous abilities themselves. They would constantly send assassins after the prodigy and try to create chaos in Konoha to keep the Anbu and the prodigy distracted while they carry out their real objectives.
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.
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.