Madara Uchiha could also be the main antagonist in this fanfiction. He might see Naruto's new Son Goku - like power as a threat to his plans of ruling the ninja world. He would try to eliminate Naruto to prevent him from using this newfound power to oppose him, and their battles would be epic with Naruto having to combine his ninja techniques with Son Goku's power.
It could be Orochimaru. He's always after power and seeing Naruto with Son Goku's power would make him a prime target. He might try to extract the power from Naruto for his own evil experiments.
Maybe a new villain from the Dragon Ball universe who follows Son Goku's power into the Naruto world. This villain could be someone who was envious of Son Goku's power and wants to take it from Naruto to prove himself superior. He would have different abilities compared to the usual Naruto villains, creating new challenges for Naruto.
Well, it could be about Naruto somehow obtaining the power of Son Goku. Maybe there's a strange jutsu that fuses their powers. Naruto could use Son Goku's strength in battles, like having his speed and ki blasts along with his own ninja skills.
It could be Orochimaru. He's always been after power and Naruto having the power of two Bijuus would be very tempting for him. He might try to extract the Bijuus from Naruto to use for his own evil purposes.
A rogue ninja who has made a pact with dark forces. He wants to use Goku's son to open a portal to the Saiyan planet and then invade it. He would be constantly trying to manipulate the situation to get Goku's son to do his bidding. He has a team of minions who are also skilled in both ninjutsu and some dark form of ki - like powers.
It could be Zamasu. Since Goku Black was Zamasu in Goku's body in the original story, perhaps a more powerful and enraged Zamasu could be the main antagonist. He might be jealous of the new fused form's power and seek to destroy it.
It could be someone who wants to use Naruto's connection to the scar for their own evil purposes. Maybe a rogue ninja who believes that the scar holds some kind of dark power that can be harnessed.
It could be a rogue ninja who has a vendetta against Naruto. This ninja might see Naruto's son as a way to get back at Naruto for past defeats or slights.
Maybe it would be a combined form of some of Naruto and Goku's most powerful enemies. For example, if Frieza and Orochimaru somehow combined their powers and knowledge. They would be a very tricky opponent for the fused Naruto - Goku as they would know the strengths and weaknesses of both heroes.
It could be someone like Madara Uchiha. He's extremely powerful and his goals are often in conflict with Naruto's. Goku would have to face his Sharingan abilities and his vast array of jutsu.
There's also the possibility that Orochimaru could be the main antagonist again. He might be intrigued by Naruto's new powers and try to experiment on him. Orochimaru is always after power and knowledge, and Naruto's Saiyan powers would be something he'd be very interested in. He could use his snake - like abilities and various jutsus to try and capture Naruto.
It could be someone who wants to use Naruto's unique heritage against him. Maybe a villain from the Naruto universe who sees Naruto's connection to Harley Quinn as a weakness. For example, Orochimaru might want to capture Naruto to study his strange combination of powers.