It could be a powerful ninja from Naruto's world who has turned evil and has found a way to travel to the One Piece world. He wants to use the power of the Devil Fruits and the ancient secrets Robin knows to take over both worlds.
The main antagonist could be an ancient being that was sealed away long ago in both the Naruto and One Piece worlds. Naruto and Robin accidentally awaken this being while exploring an ancient site. This being has the power to manipulate reality and wants to reshape both worlds according to its own dark desires.
In a different take, a new character could be introduced as the main antagonist. Maybe a criminal mastermind who teams up with the Joker specifically to target Robin. This new character could have a personal vendetta against Robin or see him as a key to achieving some greater evil plan, and the Joker is just a means to an end in this scenario.
Perhaps an ancient being that was sealed away in both worlds long ago and is now awakened. This being could be extremely powerful, seeing the combined Naruto and One Piece universes as a threat or a source of power to be harnessed for its own dark purposes. It would be a formidable foe for Naruto and the One Piece characters alike.
It could be a powerful pirate crew that doesn't like the idea of an outsider like Naruto coming into their territory. They might see him as a potential rival for treasures or influence, so they try to drive him out or even eliminate him, thus becoming the main antagonists.
It could be Kaguya Otsutsuki. Since she has powerful abilities and a thirst for power, she would see Kefla's power as a threat and Naruto's influence as something to be eliminated. She might try to manipulate events to turn the ninja world against Kefla and Naruto.
It could be someone who wants to merge their two worlds in a chaotic way. Maybe an evil scientist from Leela's world who has discovered the power of chakra and wants to use it for his own dark purposes. He could try to capture Naruto to study his chakra and use it to take over both universes.
The main antagonist could be an evil merman who wants to take over Ariel's kingdom and is also jealous of her friendship with Naruto. He might use his dark water - based magic to try and stop them.
An ancient evil force that was sealed away by Hashirama long ago could be released in Naruto's time. This entity, having a grudge against Hashirama for imprisoning it, would see Naruto as an obstacle too since he's allied with Hashirama. It could have powers that are completely unknown to the modern ninja world.
It could be Salem herself if the fanfiction focuses on Naruto trying to stop her evil plans. Since Salem has a long history of causing chaos and destruction, Naruto would see her as a force to be reckoned with and try to oppose her.
It could be a rogue ninja from an old clan who has a vendetta against both Konoha and Kumogakure. This ninja has been gathering power in secret and plans to destroy both villages to avenge his clan's past defeat at the hands of the combined forces of the two villages.
Perhaps in this fanfiction, Naruto is on a mission in his own world when a strange portal opens and leads him to the One Piece universe right where Robin is. At first, they are both cautious of each other. But as they learn about their respective powers and goals, they decide to join forces. Maybe there's a common enemy that is threatening both the ninja world and the pirate world, and together they strive to defeat it.