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.
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 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.
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.
Another plotline could involve Madara's relationships. As a girl, her interactions with other characters, especially those who knew her before the transformation, would change. Maybe there would be some romantic interests that develop in unexpected ways. Her old friends might have a hard time adjusting to the new her, and this could create some interesting character dynamics.
One possible plotline could be Naruto being captured by Orochimaru and forced to endure various genetic experiments. Maybe Orochimaru is trying to extract the power of the Nine - Tails from Naruto in a more invasive way. Another could be that Naruto's friends, like Sasuke and Sakura, attempt a daring rescue mission while Naruto is in Orochimaru's clutches and they face off against Orochimaru's minions.