A possible plotline is that Obito is trying to corrupt Naruto's friends or the new generation of ninja in the fanfiction. Naruto, being protective, hates Obito for this. Or perhaps Obito is using some dark power that Naruto fears will destroy the ninja world, and Naruto's hatred is a result of his determination to stop Obito from using that power to cause more harm.
Often, there's a plotline where Naruto and Obito are on opposite sides of a conflict within the fanfiction. Naruto is fighting for the good of the village and Obito is working against it. Naruto's hatred for Obito grows as Obito continues to cause chaos. There might also be a plotline where Naruto discovers some new, even more terrible deeds that Obito has committed, fueling his hatred further.
One common plotline is Naruto leaving the Leaf village in anger. He might then team up with former enemies who also have grudges against the Leaf. For instance, he could form an alliance with Orochimaru's followers who also have issues with the Leaf's power structure.
Some fanfictions have Naruto uncovering dark secrets about Konoha. These secrets could be about the actions of the previous Hokages or the village elders. Discovering these secrets makes Naruto lose faith in Konoha and start to hate it.
Maybe in the fanfiction, Obito makes a deal with an enemy that Naruto sees as a betrayal. So Naruto, with his strong sense of loyalty to the village and his friends, decides to abandon Obito. This could lead to a series of events where Obito tries to redeem himself in Naruto's eyes.
One common plotline could be Naruto leaving his family behind and finding a new family in his friends. For example, he might feel so estranged from his blood relatives that he decides to build a closer bond with Sasuke, Sakura, and Kakashi, seeing them as his true family. Another plotline could involve Naruto trying to discover the reasons behind his hatred. Maybe he uncovers some long - hidden family secrets that made him develop such strong negative feelings.
One common plotline is Naruto realizing Hinata's worth after some event. For example, Hinata might save Naruto from a dangerous situation, and that makes Naruto see her in a new light and start to develop stronger feelings. At the same time, he could start to distance himself from Sakura because of her continued focus on Sasuke. Another plotline could be Hinata and Naruto getting paired up for a mission, during which they bond more closely while Naruto realizes how different she is from Sakura in terms of her loyalty and selflessness.
One possible plotline could be Obito teaching Naruto some unique jutsu that he learned during his time in Akatsuki. For example, he might show Naruto how to use certain space - time ninjutsu in a different way. Another could be Obito helping Naruto understand the Uchiha clan better, given his own Uchiha heritage.
One possible plotline could be that Naruto discovers a system in his village that favors certain ninja clans over others. He then decides to fight against this system to bring equality. For instance, in terms of training resources or mission assignments.
Another plot could be that Naruto is tricked into believing a false narrative about the ninja world. Similar to how Obito was manipulated by Madara's lies. He then starts to act in ways that are contrary to his usual self. He might target the other villages, thinking he is doing the right thing for some grand, but misconstrued reason. This would lead to him being at odds with his former friends, who would be desperate to bring the old Naruto back.
In 'Naruto son of Obito fanfiction', a common theme is the exploration of destiny. Naruto's destiny is completely changed as he is now related to Obito. There is also the theme of secrecy. The fact that he is Obito's son may be kept a secret at first, and how that secret affects his relationships and the village is often explored. And of course, the theme of growth. Naruto has to grow not only as a ninja but also in understanding his new family heritage, which is different from what he thought before. This growth can involve his mental and emotional states as well as his physical abilities.
Another theme is the power of friendship. Their relationship, despite their differences, shows how friendship can bridge gaps. In some fanfictions, they start off as enemies but gradually become friends and rely on each other. This theme emphasizes the importance of having someone who believes in you, like Naruto believes in Obito's potential for good.