He could die in battle. Maybe a new, extremely powerful villain emerges who has the ability to nullify Goku's powers or is just so strong that Goku's attacks have no effect. After a long and intense fight, Goku is defeated and dies.
Well, Vegeta would be a likely character. He might be initially suspicious of the female Goku. Maybe he thinks she's a threat or just can't believe there's another Goku - like being. He could be there to add some comical moments as he tries to understand the situation.
In general, it's a bit of a toss-up. The strength of Manga Goku and Anime Goku can vary depending on the specific arcs and battles. Sometimes, it might seem like one is stronger in a particular situation, but that could change in another.
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.
One of the characters who could betray Goku is Piccolo. Although they've been allies for a long time, in fanfiction, things can change. Perhaps an ancient evil force takes control of Piccolo's mind and makes him turn on Goku. Or it could be Krillin. He might be influenced by an outside force that convinces him Goku is becoming too dangerous. Also, don't forget about the Kais. If there's some sort of power imbalance or a threat they perceive from Goku, they might betray him to maintain the order of the universe in the fanfiction.