In 'naruto meets samehada fanfiction', the main antagonist could be a new character created specifically for this story. This character could be a power - hungry being from a different dimension who senses Samehada's power across the realms. They come to the Naruto world to claim Samehada and use its power to open portals to other dimensions and rule over all of them. Naruto and his friends would have to figure out this new threat's weaknesses and stop them before it's too late.
The main antagonist might be an old enemy of the wielder of Samehada. They could target Naruto as well, thinking he's an ally of Samehada's side. This enemy could have a long - standing grudge against Samehada's power and the group associated with it. They would stop at nothing to destroy Samehada and anyone who stands in their way, including Naruto. And they might have some dark and powerful jutsus to use against them.
It could be someone who wants to steal Samehada for its power. Maybe a rogue ninja who has heard of Samehada's ability to absorb chakra and plans to use it to take over the ninja world.
Madara Uchiha would also make a great antagonist. Imagine if he was resurrected and saw Naruto with Samehada as a threat to his plans of creating a new world order. He would use his Sharingan and Rinnegan powers to try and take Samehada from Naruto, believing that with it, he could easily defeat all who oppose him and reshape the ninja world according to his will.
Well, in 'naruto meets samehada fanfiction', Naruto could potentially have a fight with the wielder of Samehada. During the battle, he might discover some new aspects of his own powers as he tries to counter Samehada's ability to absorb chakra. And it could also lead to an unexpected alliance if they face a common enemy.
Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.
It could be a powerful alchemist who has gone rogue and wants to use Naruto's chakra for some dark alchemy purpose.
It could be an evil ninja who wants to capture the fem Kyuubi for her power. He might see the unique bond between Naruto and the fem Kyuubi as a threat to his plans of world domination.
It could be Samehada itself. Since the story is about it being neglected, it makes sense for it to be the main focus. It could have its own 'voice' and thoughts as it tries to deal with the situation.
Maybe Orochimaru could be the antagonist. He hears about Naruto's encounter with Yagura and wants to use their connection for his own evil experiments. He might try to capture Yagura again (if he was once under Orochimaru's control) or manipulate Naruto into doing something that would harm Yagura and the relationship between the two villages.
It could be an evil shinobi who wants to disrupt the meeting between Naruto and Kushina. Maybe they know that Kushina has some special knowledge or power that she could pass on to Naruto, and they don't want that to happen.
It could be a rogue Sound ninja who has his own agenda. Maybe he wants to start a war between Konoha and the Sound Village to gain power in the chaos. He would see Naruto as a threat to his plans and try to eliminate him.
It could be someone who doesn't want Naruto and his sister to unite. Maybe a rogue ninja who fears their combined power. He might try to drive a wedge between them by spreading false rumors or causing misunderstandings.