Perhaps there are some within the village who oppose Naruto having a sister and see her as a threat to the status quo. These people might try to drive a wedge between Naruto and Lemon, creating internal conflict. They could be some of the more traditionalist ninja families who don't like the idea of a new, unknown element like Lemon in the village.
It could be some rogue ninjas who are after Lemon for some reason. Maybe they think she has a special power that they can use for their evil plans.
Another option is that there is an outside force, like a powerful group from another land. They hear about Naruto's growing influence and his sister, and they see them as a potential threat to their own expansion plans. So they send their agents to target Lemon and try to use her to control Naruto or simply to get rid of both of them.
Well, it could be about Naruto protecting his sister Lemon from various threats in the ninja world. Maybe they go on adventures together, with Naruto using his skills and Lemon having some unique abilities of her own.
The Akatsuki could be the main antagonists. Since Naruto is an important target for them, and if Kurenai is now his sister, they might see her as an obstacle in their way. They could try to use their various powers and strategies to either capture Naruto or cause harm to both him and Kurenai.
One possibility is a group of shinobi from a rival village. They believe that Naruto's mother held the key to some great power or secret that could give their village an edge. So, they try to either capture Naruto to extract the information or stop him from uncovering more about his mother. Another could be a dark spirit that was somehow sealed away by Naruto's mother long ago, and now it's trying to break free and take revenge on her through Naruto.
The main antagonists could be the traditional Naruto villains like Orochimaru or the Akatsuki members. They might target Naruto's sister as a way to get to Naruto, seeing her as a weakness or a way to manipulate him.
It could be Orochimaru. He has always been interested in power and the secrets of the tailed beasts. So, he might see Naruto and the Jinchuuriki family as a source of great power to experiment on or steal from.
Obviously, Naruto and his sister are the main characters. Naruto is a well - known character from the Naruto series, known for his determination and his dream of becoming Hokage. His sister, though not part of the original series in this way, would be a new character in this fanfiction with her own unique traits and abilities.
The Foot Clan could be a main antagonist. They might see the baby sister as a way to get to the turtles, either by kidnapping her or using her to blackmail them. Another could be Shredder himself if he returns. He would surely not pass up the opportunity to use the baby sister against the turtles. And Baxter Stockman could also be an antagonist. He might be interested in using the baby sister for some of his mad - scientist experiments.
One possible antagonist could be a jealous rival among the pirate gangs. This person might envy Harry Hook's sister's skills or popularity. Additionally, a corrupt official in the Isle of the Lost who wants to keep the status quo and sees her as a troublemaker could be an antagonist. Also, if there are any ancient curses or dark spirits on the isle, they could turn against her and try to stop her from achieving her goals.
Voldemort's remaining followers could be antagonists. They might target Harry's little sister thinking they can use her to get to Harry. They could try to kidnap her or use dark magic on her.
One potential antagonist could be those within the village who oppose Naruto's relationships. They might see his harem as a threat to the traditional values of the village and try to cause trouble for Naruto and his partners.