Who could be the main villain in a Naruto Secret Base Fanfiction?

Another possibility is that the main villain could be a spirit or entity that has been trapped for centuries. It uses its influence to make the Hidden Leaf Village conduct 'experiment 101' on Naruto. The spirit hopes to use Naruto's body as a vessel to be reborn into the world and wreak havoc. So it manipulates the events and people involved in the experiment from the shadows.

It could be Orochimaru. He might be interested in stealing the exosuit to enhance his own powers and immortality research. He could see the exosuit as a new way to achieve physical enhancements beyond what his current jutsu can do.

Danzo could be a great main villain in a Naruto Frankenstein fanfiction. He's always been power - hungry and secretive. He might use the concept of creating a Frankenstein - like being to gain more power for Konoha in his own twisted way, but really it's all about his own control. He could be using parts of dead ninja's abilities or something like that, and Naruto would have to stop him.

Orochimaru could be a likely main villain. He has always been interested in Naruto's power and body. Maybe he finally devises a plan to kidnap Naruto and use his body for his own reincarnation experiments.

It could be Orochimaru. He's always interested in new forms of power and experimentation. He might see Wolverine as an interesting specimen to study and try to extract his healing factor or adamantium for his own purposes. This would put him in direct conflict with both Wolverine and Naruto, who would naturally oppose Orochimaru's evil plans.

A powerful demon from another dimension could be the main villain. This demon has noticed Natsu's growing power and sees him as a threat. The demon has the ability to create illusions and false memories, which could be used to drive a wedge between Natsu and the Fairy Tail guild. He works in secret, slowly weakening Natsu's mental state before making a big move.

Madara Uchiha might be the main villain. He has powerful time - related abilities in the original series. He could use his Mangekyo Sharingan or other powers to freeze Naruto in time. His goal could be to disrupt the balance of power in the ninja world. With Naruto out of the picture, he can more easily carry out his plans to reshape the world according to his own vision. He might see Naruto as a major obstacle to his grand plan, so he freezes him to eliminate the threat.

It could be Danzo. He might have some hidden motives and manipulate situations to make Naruto look like a threat, forcing Minato to arrest him.

It could be Orochimaru. He's always been interested in obtaining power and immortality. The Blade of the Immortal would be a great addition to his collection of powerful items. He could try to steal it from Naruto if he knew Naruto had it.

Perhaps a ninja who has a grudge against Naruto because he once ate all the ramen at a festival, leaving none for the ninja. So this ninja decides to target Ichiraku Ramen and tries to put a curse on the ramen that would make anyone who eats it sick. Naruto has to figure out how to break the curse and stop the ninja.