It could be a rogue ninja who also has mastered Nen. He might be jealous of Naruto's newfound power and wants to steal it for himself.
There could be a group of antagonists. For instance, a cult of Nen users who believe that Naruto's unique combination of chakra and Nen is an abomination. They try to eliminate him and spread chaos in the Naruto world using their Nen powers. They might have various Nen abilities like manipulation, emission, and enhancement, which Naruto has to figure out how to counter as he defends his world and his friends.
Maybe an evil Nen user from another dimension comes to the Naruto world. This antagonist could be seeking to conquer the world using Nen, and Naruto, as the master of Nen in this fanfiction, stands in his way. He would have different and more powerful Nen abilities compared to Naruto at first, creating a big challenge for our hero.
Perhaps in this fanfiction, Naruto is born with the ability to use Nen, but it lies dormant until he faces a great danger. When it awakens, he has to learn to control it quickly. He might struggle at first, as Nen is very different from chakra. But with the help of his friends and his own determination, he masters Nen and uses it to protect Konoha from a new and unexpected threat that normal ninja techniques can't handle.
It could be a rogue ninja who also has strong water - based abilities and wants to prove that he is the true master of water. He might see Naruto's newfound skills as a threat.
A rogue ninja who has mastered all the dark aspects of the elements could be a great antagonist. This ninja could use their powers to create disasters, like summoning tsunamis with water element or causing volcanic eruptions with fire element. They might have a vendetta against the Hidden Leaf Village and see Naruto as a threat to their plans because of his growing elemental powers.
It could be a rogue ninja who also has some form of magnetism - based power but uses it for evil. This ninja might be jealous of Naruto's natural talent and wants to prove that he is the stronger one.
Perhaps an ancient demon that was once sealed away but has now been released due to some unforeseen circumstances. The demon has an affinity for fire and sees the Fire Master as a threat to its plans of world domination. It would constantly try to eliminate the Fire Master and anyone who stands in its way, including Naruto and his friends.
Team Rocket from the Pokemon world could be the main antagonist. They might see Naruto as a threat to their plans of stealing powerful Pokemon. They could try to use their usual sneaky tactics on Naruto, but he would be too smart for them with his ninja training.
Perhaps an ancient evil spirit that was sealed away long ago and is now awakened by the power of Spinjitzu. This spirit wants to use Spinjitzu to destroy the ninja world, and Naruto has to stop it.
It could be a rogue ninja from a hidden village who has also mastered lightning jutsu and wants to prove himself stronger than Naruto. This ninja might have a personal vendetta against Naruto or Konoha.
It could be a rogue ninja who is also a master of illusions and wants to use his powers to take over the ninja world. He might see Naruto as a threat to his plans since Naruto is developing his illusion skills.
Perhaps an old enemy from Naruto's past who has resurfaced with new and enhanced combat abilities. This enemy holds a grudge against Naruto and the Leaf Village and aims to destroy them both. He has studied Naruto's combat style and found ways to counter it, making him a formidable antagonist.