There could be a powerful wizard - like being who has the ability to control minds. He sees Goku and Goku Jr as a threat to his plans of ruling the universe. So he starts to manipulate people around Goku Jr to turn them against him, and then he faces off against Goku and Goku Jr when they come to stop his evil scheme.
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.
Obviously, Goku and Goku Jr are the main characters.
Well, it could be about Goku Jr learning some of Goku's most powerful moves. Maybe Goku teaches him the Kamehameha. They might also go on an adventure together, like fighting a new and powerful enemy that neither could face alone.
In this fanfiction, they might have an epic sparring session. Goku could pass on some of his old fighting techniques to Goku Jr.
Another possible main character could be the villain that forces the two Gokus to meet. This villain could be a new, super - powerful threat that the two Gokus need to deal with. Their meeting becomes a crucial part of the story to defeat this powerful foe.
It could be Frieza. Since Frieza has a history of hating the Saiyans, he might see Goku's sister as a new threat and try to eliminate her.
There could also be other characters from the Dragon Ball universe making an appearance. For example, Vegeta might show up. He could be curious about Fem Goku and how she compares to Goku in terms of power. Or Bulma could be there, perhaps she's interested in the technology or biology behind Fem Goku's existence.
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's hard to say. Adult Goku has more experience and has achieved higher power levels. But Kid Goku has an unbridled potential that could make him a formidable opponent even to his adult self.
There could be a power - hungry being who wants to use Goku's mother for their own gain. When Goku tries to meet her, this being tries to stop him because they know that if Goku and his mother reunite, they will be able to oppose their evil plans together.
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.