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.
In a fanfiction where Naruto becomes Obito, it could be due to an outside force. For example, an ancient evil entity that wants to disrupt the balance of the ninja world. It targets Naruto and messes with his mind, implanting Obito - like thoughts and desires. Naruto would then struggle between his original self and this new, Obito - influenced persona, leading to many internal and external conflicts within the story.
Well, Naruto could gain the power of the Juubi in many ways. Maybe through some ancient ritual or a powerful enemy's defeat that transfers the Juubi's essence to him. Once he becomes the new Juubi, his physical abilities would skyrocket. He'd have even greater chakra reserves and strength, allowing him to protect the Hidden Leaf like never before.
If Naruto turns into a super villain in fanfiction, perhaps his transformation is due to some dark influence. It could be a powerful and evil chakra that corrupts him. He would then start to use his jutsu in cruel and unexpected ways. For example, instead of using the Rasengan to protect, he might use it to destroy important buildings or harm innocent people. His friends would be shocked and try to bring him back to the good side, but he would be too far gone. This could lead to some really intense battles and emotional confrontations between him and his former comrades.
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.
Well, in such a fanfiction, Naruto being a Kryptonian would mean he has heat vision. This new power could be used in battles against the Akatsuki. Instead of using Rasengan, he could simply use his heat vision to take out opponents. Also, his invulnerability would make him a force to be reckoned with. He could walk through most attacks without a scratch. His character might also change as he has to deal with these new powers and the responsibility that comes with them. It's an interesting concept that would mix the Naruto world with the Kryptonian lore.
If Naruto loses all his friends in a tragic way, perhaps in a battle against an overwhelming enemy that the village could have prevented. His grief could turn into hatred towards the shinobi system. He may decide that the existing order is what causes all this pain and destruction, and then he starts to work against it, becoming a villain in the eyes of the village.
Well, if Naruto were to create an Akatsuki fanfiction, one way the storyline could develop is by having Naruto try to understand the motives of the Akatsuki members more deeply. He might explore the idea of redemption for some of them. For example, he could write about how Pain, after seeing the destruction he caused, might have a change of heart. Naruto could also create scenarios where the Akatsuki members interact with the villagers of Konoha in a more positive light, like how Sasori could use his puppet - making skills to help the kids in the village create toys instead of weapons.
Well, one way the storyline could develop is that Naruto's immortality would give him an edge in the wizarding world. He could use his ninja skills along with newfound magic abilities. Maybe he'd be a bit of an outlier in Hogwarts, not fully understanding the magic system at first but quickly adapting due to his ninja training. His immortality might make some dark wizards target him, thinking he holds some sort of secret to eternal life. And he'd probably form unique friendships, like with Harry, Ron and Hermione, teaching them some ninja moves in return for magic lessons.
It could start with Naruto being sent on a mission to an unknown realm. There, he meets someone who is very much like the Red Hood. They team up and Naruto learns about the Red Hood's ideology. Over time, he realizes that he can better protect this new world by becoming like the Red Hood. He would then start training in the Red Hood's combat style while still having his ninja abilities as an advantage.
Well, in this fanfiction, Naruto might become a chef because he wants to bring people together through food. Since he's always been about unity, he could start a small eatery where people from different villages can come and enjoy a meal. He'd probably make dishes that are inspired by his travels. He could incorporate different elements from the places he's visited during his ninja missions. Also, his friends like Sasuke and Sakura might be his first customers and give him feedback. Naruto would be the kind of chef who puts his heart into every dish, just like he put his heart into protecting the village.