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.
It could be Orochimaru. He's always been interested in power and experimenting. Maybe he sees Naruto as a perfect guinea pig to test some new jutsu that goes horribly wrong and causes Naruto to explode.
It could be Danzo. He has always been a bit of a shadowy figure with his own motives in the Naruto series. He might see Naruto as a threat to his power and influence within the village and engineer a situation where Naruto is executed.
It could be Madara Uchiha. He was always seeking power and new ways to achieve his goals. Turning Naruto into a weapon would be a great advantage for him in his plans to reshape the ninja world.
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.
It could be Orochimaru. He has always been interested in Naruto's power. Maybe he locked Naruto in a cage to study his chakra or to use him in some kind of dark experiment.
A new and powerful rogue ninja could be responsible. This ninja might have a vendetta against Konoha and see Naruto as a symbol of the village, so they target him and use their strong and devious techniques to injure him badly.
Another possibility is that a rival pirate group that has a long - standing feud with the Whitebeard Pirates managed to finally get the upper hand and capture Marco. They could have been studying his movements for a long time and found a weakness in his defenses. This group might be led by a very cunning and powerful pirate captain who has a personal vendetta against the Whitebeard Pirates and sees capturing Marco as a major victory.
The village elders are likely candidates. They are often shown to be power - hungry and manipulative in the Naruto series. They might see Naruto's power as a threat to their control over Konoha and thus plot against him, which could lead to Naruto feeling betrayed.
A rogue ninja from a rival village could be responsible. They might see Naruto as a threat and use their fire - based attacks to harm him. For instance, a ninja from the Hidden Mist Village who has a grudge against Konoha and targets Naruto specifically.