Another option for the main antagonist could be an ancient being that was sealed away long ago. Now that Naruto and Goku are fused and causing a disturbance in the energy balance of the universe, it wakes up. It has powers that are completely different from what Naruto and Goku are used to, so they would have to adapt quickly to fight it.
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 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 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.
In this fanfiction plot, a powerful sorcerer or some sort of interdimensional being could be the cause of the fusion. The fused Naruto - Goku would have an insane amount of power. They could travel at super - fast speeds like Goku and also use shadow clones like Naruto. Their power level would be off the charts. They might end up in different parts of the new world they're in, trying to find each other and figure out what happened, all while being chased by enemies who want to study or destroy their new form.
Maybe an old enemy of Goku's who has somehow managed to return. This enemy has heard about Goku Jr and figures that by attacking him, he can get revenge on Goku. This could be someone like Frieza who has found a new way to be resurrected and is more powerful than ever.
Their fused form might have Goku's spiky hair, but with some of Goku Black's purple - tinted highlights. The body would be muscular like Goku's, but with a more menacing stance similar to Goku Black. The clothing could be a combination of Goku's orange gi and Goku Black's black under - shirt, maybe with some red accents added in for an extra pop of color.
In fanfiction, if Goku Black fused with Goku, it could potentially create an extremely powerful being. This new entity might have a mix of Goku's pure heart and Goku Black's more sinister motives, which could lead to a complex internal struggle. Their combined power could be off the charts, perhaps strong enough to defeat any foe in the Dragon Ball universe. However, it could also cause chaos as their different personalities clash within the fused form.
The Locust Queen could still be the main antagonist. Goku would see her as a great threat to the people of Sera. His sense of justice would drive him to take her on directly.
Maybe a mad scientist - type character who has created a device that can disrupt the fabric of reality. He wants to use it to reshape the universes to his own liking. Goku and Lemon get in his way because they are trying to protect their respective homes. The scientist is constantly evolving his device and creating new threats for Goku and Lemon to overcome.
In a 'Harry Potter trained by Goku' fanfiction, the main antagonist could be an evil wizard who has allied himself with dark forces from other dimensions. This wizard could see Harry, with his new skills from Goku's training, as a major threat to his plans of world domination. He might have powers that are a mix of dark magic and some sort of energy manipulation similar to ki. Harry would then have to use his combined magic and Goku - trained skills to take on this powerful and devious enemy.