Perhaps in this fanfiction, Sasuke captures Naruto because he has been influenced by some dark force. This could lead to a struggle within Sasuke between his old friendship with Naruto and the new, darker desires that the force has instilled in him. Naruto, being captured, would then have to try and reach the old Sasuke within and break the hold of this dark influence.
Well, it could be that Sasuke captures Naruto as part of a plan to protect him from a greater threat that Naruto is unaware of. Maybe Sasuke has some inside information about a powerful enemy who is targeting Naruto, and by 'capturing' him, he can keep Naruto in a safe place until the danger passes.
Well, Naruto might be interrogated for information about the Hidden Leaf. The Akatsuki are always after secrets, especially about the Jinchuriki. So they could be trying to find out more about the Nine - Tails within Naruto.
Well, he could be tortured for information about Konoha. The Iwa ninjas might try to extract secrets about new jutsus or strategic plans. They could also use him as a bargaining chip against Konoha.
One possibility is that Naruto is being captured for a misunderstanding. Maybe Konoha has received false information about Naruto being a threat. In the fanfiction, this could lead to his friends having to prove his innocence.
Well, if Naruto is captured by Orochimaru in fanfiction, one possibility is that Orochimaru wants to use Naruto as a bargaining chip against Konoha. He may think that by having Naruto in his grasp, he can force the Hidden Leaf to meet his demands, like giving him access to certain forbidden jutsu or secret scrolls. Another aspect could be Orochimaru's curiosity about Naruto's ability to master new jutsu so quickly. He might want to study Naruto's mind and body to find out the secret behind his growth as a ninja.
Well, one possibility is that Naruto's friends would immediately start a rescue mission. They'd gather all the intel they can about Kumo's defenses and where Naruto is being held. Maybe Sasuke would put aside his differences for the time being and team up with the others.
If they are cousins in fanfiction, it could change the whole dynamic of the ninja world. Their combined strength as family members could be a threat to their enemies. They might be able to use their family connection to bring peace to the villages in a different way. Maybe they could form a new kind of alliance based on family rather than just friendship or rivalry. And this could inspire other ninja clans to also seek peace through family connections.
It might be for Naruto's own good. Sasuke may believe that Naruto is on a dangerous path that will lead to his downfall. So he captures him to keep him from making bad decisions, like sacrificing himself for the village or something similar. He wants to save Naruto from himself in a sense.
In such a fanfic, Naruto might be subjected to various interrogations by Kumo. They could be interested in his Nine - Tails power. Maybe they would try to extract information about Konoha's secrets through him.
In this fanfiction scenario, their teamwork could reach a new height. Hagoromo would likely train them together, so they would understand each other's strengths and weaknesses better. Naruto's optimism and Sasuke's more brooding nature could be balanced out under Hagoromo's guidance. They might also learn new joint - attack techniques. For example, they could combine Naruto's Rasengan and Sasuke's Chidori in a way that is more powerful and versatile than before. Their bond as friends and comrades would be strengthened, and they would be better equipped to face any future threats to the ninja world.
There could be a situation where the inn is under attack by a common enemy. Itachi, Sasuke and Naruto have to put aside their differences and work together to defend it. They use their unique skills - Itachi's genjutsu, Sasuke's fire - based jutsu and Naruto's shadow clones - to fend off the attackers. This experience bonds them in a new way and they leave the inn with a newfound respect for each other.