Perhaps Naruto seals himself away due to a prophecy. He might believe that by doing so, he can prevent a greater catastrophe in the future. His friends and the village might initially oppose this decision but eventually come to understand its necessity as they uncover more about the prophecy and the threats it foretells.
One possible plot development could be that the village is in great danger from an enemy too powerful to defeat directly. Naruto, seeing no other way, seals himself away to act as a last - line - of - defense deterrent. If the enemy tries to completely destroy the village, Naruto's sealed power could be unleashed to counter them.
It could be a new and extremely powerful ninja from a far - off land who has a vendetta against Konoha. His power might be so great that Naruto decides the only way to stop him in the long run is to seal himself away as a sort of trap for when the antagonist gets too close to achieving his goals.
In a fanfiction where Naruto is sealed away, there could be a focus on the emotional turmoil of his friends and family. Hinata, for example, might be extremely distraught and use her Byakugan in new ways to try and find Naruto. Sasuke could also return to the Leaf Village out of loyalty to Naruto and join the efforts to unseal him. The story could also explore how the younger generation of ninjas, inspired by Naruto's legacy, strive to become stronger to free him.
Perhaps Naruto was in a situation where he had made a deal. For example, he promised to pay for the seals in exchange for some information about a missing nin or a secret technique. He values knowledge and power, and if paying for the seals was part of getting closer to achieving his goals, he would do it.
One possible plot development could be that Sasuke is initially in a situation where he is facing an enemy he can't defeat alone. Naruto steps in and gives his life to save Sasuke. This would lead to Sasuke being filled with guilt and a new sense of purpose. He might vow to carry on Naruto's will, perhaps trying to bring peace to the ninja world in Naruto's name. Sasuke could also start to question his own actions that led to Naruto having to sacrifice himself, and he may become more empathetic towards others as a result.
In this fanfiction, Peter might have discovered some dark secret about himself or his world. He locks himself away to protect others from it or to come to terms with it on his own. He could be in a world full of magic or superpowers, and this secret is related to that. He needs time alone to understand how to control it or whether to reveal it.
It could also be that Dolohov's desire for Hermione causes a rift among the Death Eaters. Some might see it as a distraction or a sign of weakness. This internal conflict within the Death Eaters could then be exploited by Hermione and her allies to their advantage in the fight against the dark side.
One possible plot development could be Naruto using his new jutsu to break Yugito free from an enemy's trap. Another could be that Naruto's words break Yugito's negative mindset.
There could be a split in the ninja world. Some might see Naruto as a savior with his new power, believing he can protect them from greater threats. Others, however, might fear that he will become a dictator with such immense power. This could lead to internal conflicts within the villages, with Naruto caught in the middle, trying to prove that he will use his power for good.
A possible plot development could be that Naruto's connection to the Nine - Tailed Fox gives him an advantage in a situation where Shirou was at a disadvantage. For example, if there was a powerful dark force in the story, Naruto could use the Nine - Tailed Fox's power to fight it off, while Shirou might have struggled more. Also, Naruto's charisma could attract different allies compared to Shirou, and these new allies could bring in their own sub - plots and story arcs.
In the 'naruto has no eyes fanfiction', the plot might involve Naruto discovering a new form of chakra that is unique to his condition. This new chakra could give him abilities that he didn't have before, like the ability to sense the emotions of his opponents. There could also be a plot twist where Naruto's blindness is actually a part of a greater prophecy, and he has to fulfill it in a way that no one expected.