Perhaps a major plot twist could be that Naruto's true origin was hidden to protect him. In the fanfiction, it could be revealed that Shisui had some sort of premonition about the Uchiha massacre and sent Naruto away to be raised in secret. As Naruto grows up and discovers his true relation to Shisui, he has to grapple with his new identity and the responsibility that comes with it. He may also be the key to preventing future tragedies related to the Uchiha clan.
A plot twist could be related to the Uchiha clan's perception of Naruto. Normally, Naruto is an outsider to the Uchiha, but as Shisui's younger brother, he would be part of the clan. This could lead to internal power struggles within the Uchiha, with some seeing Naruto as a threat due to his connection to Shisui and his own growing power. It could also change Naruto's relationship with Sasuke, as they would now have a different family - like connection through Shisui.
One possible plot twist could be that Naruto inherits some of Shisui's unique abilities. Since Shisui was known for his powerful Sharingan techniques, Naruto might develop a new form of jutsu that combines his own chakra control with the Sharingan - like skills he could potentially inherit. This would make him an even more formidable ninja in the story.
Perhaps the plot twist is that Shisui faked his death not just to protect the village in the general sense, but specifically to keep Naruto safe. He knew of Naruto's importance as the Jinchuriki of the Nine - Tails and his relation to Naruto as a brother. So, he went into hiding and has been secretly guiding Naruto from the shadows all along. This would add a whole new layer to Naruto's journey and the events that have unfolded in the series so far.
In this fanfiction, a great plot twist could be related to Percy's origin. What if Percy wasn't really born in the normal way as a god's offspring? He could be a product of some ancient magic that Zeus unknowingly participated in. This revelation could shake the very foundation of the relationship between Percy and Zeus. Also, Percy might discover a hidden side of Zeus' past that Zeus has been trying to keep secret. This knowledge could put Percy in a dangerous position as he decides what to do with this information, whether to expose Zeus or keep it to himself for the sake of their relationship.
One possible plot twist could be that the pregnancy is a result of some sort of experimental jutsu gone wrong. Maybe they were trying to save someone and the jutsu had an unexpected side effect on Sakura. Another twist could be that there is some mystery behind who the father really is, even though it seems to be Shisui at first. There could be an enemy who has the ability to manipulate memories and create false impressions of events.
One possible plot twist could be that Naruto has some hidden Senju abilities due to his relation to Hashirama. This could change the power dynamics in the ninja world. Maybe he could use Mokuton (Wood Style) more effectively than Yamato. Another twist might be in the political arena. His connection to Hashirama could make him a target or a key figure in disputes between different ninja clans. And it could also change his relationship with Sasuke, as Sasuke might view Naruto's newfound heritage in a different light.
One possible plot twist could be that Naruto discovers some hidden power within himself related to his connection with Anko. Maybe it's a special jutsu that only their family line can use. This discovery could lead him on a new journey to master this power and uncover the secrets of their family's past.
One possible plot twist could be that Naruto's connection to Kurumu reveals a hidden power within him. Maybe it has something to do with a long - forgotten family heritage that Kurumu's family also shares. This could lead to Naruto having to master new abilities that are different from his regular ninja skills.
One possible plot twist could be that Naruto, despite being trained by Shisui and Itachi, struggles with the darker aspects of their teachings. For example, he might find it hard to adapt to their more stealthy and sometimes morally ambiguous tactics. Another twist could be that an enemy figures out Naruto's new training sources and uses it against him by setting traps based on the Uchiha's fighting styles. Also, Naruto could discover a hidden connection between the Uchiha clan and his own Uzumaki heritage during the training process that changes his perspective on his powers and destiny.
In this fanfiction, a really interesting plot twist could be that the training by Shisui actually awakens a dormant power within Naruto that has nothing to do with the Sharingan at first glance. As Naruto delves deeper into the Sharingan training, he starts to notice connections between this new power and the Sharingan. Maybe it's a power related to the Sage of Six Paths that gets activated in a unique way due to the Sharingan training. Also, the relationship between Naruto and Shisui could take an unexpected turn. Instead of just a teacher - student relationship, they could become something like comrades with a shared mission that is revealed during the training process.
Perhaps a plot twist could involve Naruto's parents. If Naruto is Tsunade's little brother, then it might change the story of how his parents met and what their relationship was to Tsunade. Maybe his father was involved in some sort of mission with Tsunade and that's how Naruto came to be. It would also add a whole new layer to Naruto's relationship with Jiraiya, as Jiraiya was also connected to both Naruto's father and Tsunade in different ways.
In this scenario, Naruto being Shisui's brother would mean he might have grown up with a different kind of training. Shisui was highly skilled in the ways of the ninja. Naruto could have learned some of his stealth and combat techniques at an earlier age. This would make him an even more formidable opponent. Moreover, it could have an impact on the Akatsuki's plans. They were after the Sharingan, and if Naruto was related to Shisui, they might target him differently. It could also change the way the village of Konoha views Naruto. He would have a stronger connection to the Uchiha, which could either make them more suspicious of him or more protective, depending on how the story unfolds.