Maybe the plot could revolve around Naruto getting influenced by a powerful and evil entity. This entity could corrupt his mind, making him believe that the only way to achieve true peace is through domination. So, he would begin to gather power, using his skills and charisma, but for the wrong reasons. He would form his own group of followers, who also believe in his new 'world order' ideas, and start a war against the existing shinobi villages.
If Naruto becomes a villain in the DC crossover, he might set his sights on Superman. Naruto could believe that Superman's power is a threat to the balance he wants to create. He would use his ninjutsu to try and take on Superman. For example, he could use his Rasengan, a powerful spinning ball of chakra. However, Superman's strength and heat vision would be tough for Naruto to overcome. This would lead to an epic battle between the two, with the other DC heroes and Naruto's possible allies getting involved as well.
Batman would definitely be one of the most affected. He's used to dealing with normal threats in Gotham, and Naruto's supernatural abilities would be a huge challenge. Another would be the Flash. Naruto's clones could potentially surround and confuse the Flash. Wonder Woman too. She's a warrior, but Naruto's unorthodox fighting style and his array of jutsu would be difficult for her to counter immediately.
It could be Sam and Tucker. Since Danny has become a villain, his former friends would likely try to stop him. They would be the main antagonists from Danny's point of view now. They would use their knowledge of Danny and their own skills to try and bring him back to the good side.
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I strongly recommend Naruto in One Piece World to you. It tells the story of a college student who likes to watch movies, anime, and play games. He transmigrated into the Naruto world and became a villain. He didn't have a cheat code, but he relied on the Naruto storyline that he was familiar with. He dodged the attacks of the main characters in one disaster after another and finally became an elite Chuunin. However, in the end, he was actually killed by Nine-Tailed's big butt when he attacked the village. What was even more deceptive was that he had transmigrated to the world of One Piece and had a speechless system. The plot of this novel was wonderful, and the characters were vivid. It was very worth reading. I hope you like this fairy's recommendation. Muah ~😗
The Joker could be a great villain. Imagine if the Joker - like character emerged in the My Hero Academia world. Izuku, with his new Batman - inspired skills, would have to use his wits to outsmart this chaotic and unpredictable foe.
In a 'Danny Phantom becomes villain' fanfiction, it could be that Danny has a major falling out with his friends and family. He feels betrayed and abandoned. This emotional turmoil causes him to snap and turn to the dark side. He then uses his ghost powers to take revenge on those who he thinks have wronged him, becoming a feared villain in the process.
Kaguya could be an interesting choice. She is extremely powerful and has a complex backstory. Her motives were initially self - serving and evil. If she were somehow resurrected or a situation where Naruto had to interact with her in a different time - line, it could make for a great fanfiction. Naruto's ideology of peace and friendship could clash and then potentially influence her.
One possible scenario could be that Naruto is transported to the Flash's universe and somehow gains the powers of Savitar. He might use Savitar's speed in his own unique way, like combining it with his shadow clones to create a sort of blitzkrieg attack. Maybe he would also struggle with the darker aspects of Savitar's power, as Naruto is typically a more positive - minded character.