It could be a new character created specifically for the fanfiction. Maybe a powerful being from a different dimension who sees Naruto's new perfect life form as a threat to his own plans of domination.
It could be a powerful devil who sees Naruto as a threat to his rule in the devil realm. Maybe this devil wants to use Naruto's power for his own evil purposes and Naruto has to resist.
Perhaps an old, powerful shinobi who was thought to be dead but has now returned in Naruto's new life. This shinobi could be seeking to reshape the ninja world according to his own dark vision, and Naruto would have to stop him. The antagonist might have some connection to Naruto's past life that is gradually revealed as the story progresses.
Maybe a new, unknown character. This character could be from a long - lost clan that has a connection to the Book of Life. They believe that the book should be used in a way that Naruto and the other ninjas don't agree with, like using it to rule over all the ninja villages.
The main antagonist could be a corrupted version of Naruto himself from an alternate timeline. This 'evil Naruto' has different ideals and is bent on ruling the ninja world with an iron fist. In Naruto's second life, he has to not only face this powerful version of himself but also figure out how to stop his own dark tendencies from emerging.
It could be Orochimaru. He is always looking for ways to gain power and in a game - like scenario, he could be the main villain trying to stop Naruto from achieving his goals. He might set up various game - like traps and challenges for Naruto.
Perhaps a powerful figure in the Naruto world who senses Naruto's newfound memories and abilities from his past life and sees him as a threat. This could be a rogue ninja or even a hidden power within the ninja villages. They might try to stop Naruto from fully exploring and using his past - life powers.
Kabuto could also be a good antagonist. After he gained all those powers and knowledge, he might target Naruto's six - tails form. He could use his medical ninjutsu to try and manipulate Naruto's transformation or even try to extract the power of the six - tails for his own use. Since he has the ability to mimic other ninja's techniques, he could be a formidable foe against Naruto in six - tails form.
Maybe an akumatized version of a weather forecaster or a meteorologist. Frustrated by always being wrong about the weather or not being taken seriously, Hawkmoth akumatizes them. They then use their knowledge of the weather and new - found powers to create the perfect storm and cause havoc in Paris, making them a formidable antagonist for Ladybug and Chat Noir.
It could be a rogue ninja from another village who has a vendetta against Naruto for his past actions in his first life. This ninja might see Naruto's second chance as an opportunity to finally get revenge.
It could be Orochimaru. In this fanfic, he could be a player of the same 'life - game' as Naruto, but with a much more sinister goal. He might be trying to manipulate the game rules to his advantage, like finding a way to make all the ninja in Konoha his puppets. Naruto would then have to figure out how to stop Orochimaru's evil plans within the game - like mechanics of his world.