A group of outcast ninja who have been wronged by the Hidden Leaf Village in the past might be the captors. They see Naruto as a symbol of the village that wronged them and Itachi as a powerful Uchiha. Capturing them would be their way of getting revenge on the village.
It could be the Marines. They've been after Luffy for a long time, so it's possible they finally manage to capture him in this fanfiction.
It could be the League of Villains. They've always been interested in taking down heroes and Deku, as a rising hero, would be a prime target for them.
The captors could be Orochimaru. He is always interested in powerful ninja and their abilities. Since female Naruto would be a very powerful individual, he might capture her to study her abilities or try to extract the Nine - Tails' chakra from her. Another possibility could be a group of anti - Konoha rebels who see Naruto as a symbol of Konoha's strength and want to weaken the village by capturing her.
The Hidden Stone Village might be the captors in some fanfictions. If there was a political struggle or a misunderstanding, they could see Naruto as a weapon of Konoha that needs to be neutralized. Their earth - style jutsus could be used to create inescapable prisons for Naruto, and they might use various interrogation techniques as torture to find out Konoha's secrets.
The Thanagarians could be the captors. They are an alien race with advanced technology. If they perceive Wonder Woman as a threat to their interests in Earth or the universe, they might capture her. Also, an ancient, long - forgotten race of demons could rise from the underworld and capture her. They might want to use her as a key to unlock some sort of dark power that has been sealed away for centuries. This would create a really interesting and spooky fanfiction scenario.
Maybe a group of rogue Pokémon hunters. These are people who don't follow the normal rules of Pokémon catching. They might be after Darkri because it's a rare and powerful Legendary Pokémon. They could sell Darkri on the black market or use its powers for their own gain, like using its dream - related abilities to find hidden treasures that are only revealed in dreams.
Maybe a rogue ninja group that wants to sell Naruto to the highest bidder. They see him as a valuable asset due to his strength and status in Konoha.
It could be other villages as well. Since Naruto has made friends and allies from different villages during his adventures. For example, the Sand Village might send some of their ninja to help, considering Naruto's relationship with Gaara.
Sasuke could be a likely candidate. Despite their differences, Sasuke and Naruto have a deep connection. He might hear about Naruto's capture and come to his rescue, driven by their past friendship and the rivalry that also binds them.
Maybe some of the more conservative village elders. They have always been a bit wary of Naruto because of the Nine - Tails inside him. So they might be behind his capture in the fanfiction.