One possible plotline could be that Naruto is constantly shunned and mistreated by the village despite his efforts to protect it. This continuous rejection could gradually turn his heart cold and make him seek revenge. He might start using his powerful jutsu against those who once wronged him, like attacking the Hidden Leaf's leadership.
It could be that Naruto is influenced by a powerful and evil entity. Perhaps an ancient demon or a rogue ninja with strong mind - control abilities gets a hold of Naruto. Under this influence, he starts to carry out evil deeds, like assassinating important figures in other villages to start wars, which is completely against his original nature.
One possible plotline could be that Harry discovers a dark secret about his family and feels betrayed by the wizarding world. This could lead him to side with the dark forces. Another could be that he is influenced by a powerful dark wizard who manipulates his mind. Maybe he becomes envious of the power others hold and decides to take it by any means, turning evil in the process.
Perhaps in the fanfic, Naruto turns into a dragon as a result of a forbidden jutsu gone wrong. In his dragon form, he discovers a connection to an ancient dragon spirit that guides him. This spirit could teach him new abilities and knowledge. His friends, like Sasuke and Sakura, would then have to help him figure out how to reverse the transformation or at least learn to live with it. They could go on a journey to find a way to control the dragon within Naruto, facing various challenges along the way, such as other ninja clans who see Naruto's new form as a threat.
One possible plotline could be that Twilight is influenced by a powerful dark magic artifact. Maybe she discovers an ancient book that slowly corrupts her mind, making her turn against her friends. As she turns evil, she might start to use her powerful magic to take over Ponyville, believing that she can create a 'better' world under her rule.
Well, a cool plotline could be Naruto using her new female form to her advantage in missions. Maybe she can infiltrate places more easily as a girl. Also, there could be a plot where Naruto has to hide the fact that she was once a boy from some new characters she meets. This could lead to some really funny or tense situations as she tries to keep her secret while still being herself.
One possible plotline could be Naruto getting corrupted by an ancient and powerful evil entity. This entity could influence him to turn against Konoha and start his reign of terror. He might use his knowledge of the village's secrets to his advantage in causing destruction.
One possible plotline could be that Naruto is influenced by some dark force and turns 'evil'. Kushina, having come back to life somehow, tries to understand what has happened to her son. She then embarks on a journey to find a way to reverse the effects, leading to a series of adventures where they interact in different ways, like Kushina trying to jog Naruto's memories of their family bond.
Well, it could be that Chichi is betrayed by her friends and that turns her evil. Maybe she discovers some dark secrets about her past that make her lose faith in good. Or perhaps she is influenced by an evil force that corrupts her pure heart.
One possible plotline could be that Naruto, under some dark influence, decides to oppose the Justice League. He might use his ninja skills and powers in unexpected and malicious ways against the heroes of the Justice League.
One possibility could be that they turn evil due to a powerful enemy using some dark magic or jutsu on them. This could make them lose their sense of self and start causing chaos in the Hidden Leaf. For example, they might start attacking their former friends and allies, believing they are now enemies.
One possible plot could be Ruby being betrayed by her closest friends. Maybe she discovers a dark secret about the Huntsman academies that makes her question everything she has ever believed in. This disillusionment could start her on the path to evil as she feels that the system she has dedicated her life to is corrupt.