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.
In a 'naruto gets captured' fanfiction, he might be tortured for information. His captors could be after the secrets of his Nine - Tails chakra. They may try to use him as a bargaining chip against Konoha.
Maybe Naruto is captured by a powerful and mysterious foe. This enemy blinds him as a form of torture. Naruto's friends and allies in Konoha soon notice his absence and begin a search. Naruto, while in captivity, tries to figure out the motives of his captors. He also tries to find ways to escape, using his chakra to sense his surroundings despite his blindness.
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.
In a fanfiction, they could be involved in a race. Naruto's speed, Sasuke's sharingan - enhanced perception, and Hinata's byakugan - aided navigation could all play a part. Maybe they start off competing against each other but then realize that there's an outside threat during the race. So they put aside their differences and work together to overcome the threat, forging a stronger bond in the process.
In this kind of fanfiction, one possibility is that they go on a journey to discover new jutsu together. They might leave the Hidden Leaf Village to find a place where they can train without the constraints of the village rules. Maybe they encounter new and powerful enemies that force them to rely on each other more than ever, strengthening their bond.
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.