Who could be the main villains in Naruto secret agent fanfiction?

The Malfoys could be the main villains. They might have turned to even darker magic after the fall of Voldemort and formed their own secret organization. Lucius Malfoy could be using his wealth and influence to gather dark wizards and witches to create chaos in the wizarding world.

The Death Eaters could also be major villains. They might team up with some anti - SHIELD groups in the muggle world. The Death Eaters' dark magic combined with the muggle - world weaponry of these groups could pose a serious threat to both the wizarding and muggle worlds that Harry and SHIELD have to stop.

The demons from Inuyasha's world that resent the idea of a half - human, half - demon having such a powerful combination of abilities could be villains. They might see Naruto as a threat to their existence or way of life and try to eliminate him. Also, there could be ninja who are jealous of Naruto's newfound powers and team up with these demons to take him down.

It could be a new character created specifically for this fanfiction. Maybe a ninja who made a deal with the forces of hell in order to gain power and now has to serve as an agent. This character would be conflicted between their newfound power and the consequences of serving hell.

The traditional village leaders who are set in their ways could be antagonists. They might see Naruto's chaos - inducing actions as a threat to their power and order.

Orochimaru could be like the Joker. He's already a bit of a mad scientist and likes to play with people's lives. Just as the Joker likes to create chaos, Orochimaru could do the same in Konoha, and Naruto, as the Batman - inspired hero, would have to stop him. He could also have some henchmen like the Joker does.

Perhaps her main adversaries are a secret society within the wizarding world that has been operating in the shadows for centuries. This society might be made up of powerful and influential wizards who believe in a different order, one that involves subjugating non - pure - blood wizards. Hermione, with her Muggle - born status, is a prime target for them. They would try to undermine her at every turn, using their vast resources and political influence within the wizarding community. Hermione would have to fight not only their magic but also their attempts to smear her reputation.

The Akatsuki could still be major villains, but with a twist. They could be interested in Naruto's connection to Iron Man and his technology. Maybe they want to use it to enhance their own powers or to create a new type of bijuu using Stark's technology. Another option could be a new villain from the Iron Man universe, like Justin Hammer, who finds his way into the Naruto world and decides to use the chaos there to his advantage by creating his own criminal empire using ninja and technology combined.

Well, the Kingpin could be a main villain. He could see Naruto as a threat to his criminal empire in New York. He might hire some ninja mercenaries from the Naruto universe to take him down. And then there's Electro, who could be enhanced by some sort of chakra - based technology. He could use his new powers to cause chaos in the city and target Naruto specifically, thinking that he's the key to getting even more power.

It could be a variety of villains. Maybe some of the traditional Naruto villains like Orochimaru or Pain could be in the story and Naruto kills them. Or perhaps in this fanfiction crossover, there are new villains created that are a combination of Naruto - style threats and Justice League - type menaces. It's hard to say exactly without reading the fanfiction, but it would be interesting if it included some well - known Naruto baddies being taken out by Naruto in a new setting with the Justice League around.