In some fanfictions, the main antagonist could be Naruto's own inner demons brought on by the presence of the wolf. These could manifest as self - doubt, fear, or a dark side of his personality that the wolf's power seems to amplify. So, in a way, Naruto has to fight against himself as well as any external threats.
In many such fanfictions, it could be a variety of deities. It might be an ancient and powerful god from Naruto's world's mythology that the story's author has chosen to insert. For example, it could be a god of elements like a super - powerful fire god, which could give Naruto even more control over his existing fire - based jutsu and new, more extreme abilities related to fire.
I'm not entirely sure if there is a specific fanfiction with exactly that premise. However, given the popularity of both Naruto and the concept of sealing powerful entities in Naruto's world, it's quite possible. Fanfiction writers love to experiment with combining different fictional elements, so it wouldn't be surprising if someone has written a story where Jenova is sealed in Naruto. You can try searching on popular fanfiction websites like Fanfiction.net or Archive of Our Own to find out for sure.
In some fanfictions of this kind, the wolf sealed in Naruto might have a past connection to a long - lost clan or an ancient evil. This could lead to Naruto uncovering secrets about the ninja world that were previously unknown. Maybe the wolf was sealed for a reason related to protecting a powerful artifact or prophecy, and Naruto now has to deal with the consequences of that.
Maybe there is an ancient wolf demon spirit that is corrupted and sees Naruto as a threat to its reign. This spirit would try to either kill Naruto or corrupt him further, causing chaos in the world.
It could be Orochimaru. He's always interested in strange and powerful forms, and Naruto's new wolf - bijuu form would be something he'd want to study or even control for his own evil purposes.
With his enemies, it would be a whole different story. They might be more cautious about attacking Naruto. Some might even try to find a way to use the god sealed in him for their own purposes. And Naruto's relationship with the hidden villages could also change. They might see him as a potential threat or a very valuable asset.
Well, Naruto might become more mysterious. Since Gaster is an unknown and rather enigmatic entity, Naruto could start having strange thoughts or powers that he doesn't fully understand at first. He might seem more withdrawn as he tries to figure out what's going on inside him, and his normal cheerful and straightforward personality could be clouded by the presence of Gaster.
There might be new antagonists created specifically for this fanfiction. They could be characters who are after the boosted gear for their own evil purposes. Maybe they want to use it to take over the ninja world or something. These new antagonists would likely have their own unique powers and abilities that would make them a challenge for Naruto and his friends.
The Akatsuki might also be the main antagonists. They were after the bijuu in the original story. With Naruto having two, they would surely target him. They might see it as an opportunity to gain an even greater edge in their plan to control the world.
His abilities would change in multiple ways. Firstly, his chakra control might be affected. Since Godzilla is a massive and powerful entity, it could disrupt Naruto's normal chakra flow. However, he could also learn to harness Godzilla's power within him. For example, he might be able to use Godzilla's raw strength to enhance his Sage Mode or even his Nine - Tails transformation. This could make him an even more formidable opponent. His speed could also be enhanced as Godzilla's power might give him a boost in his physical capabilities, allowing him to move faster and react quicker in battle.