In this fanfiction, perhaps they could have an epic battle against a common enemy. Jotaro with his Star Platinum and Jonathan with his Hamon could combine their powers in a unique way.
DIO could be a likely villain. Since he has a long - standing feud with the Joestar family. He might try to take advantage of the situation where Jotaro and Jonathan meet to cause chaos and try to defeat them both.
Well, they might have an epic showdown at first. Jotaro with his Star Platinum and McCree with his Peacekeeper. But then they could realize they have a common enemy and team up. Maybe they'd exchange stories about their different worlds.
A plot twist might be that Jotaro loses his Stand abilities temporarily and McCree has to protect him. Or perhaps they find out that there's a traitor among the people they thought were their allies in this fanfiction world. This would force them to re - evaluate their situation and who they can trust. Also, it could be that a powerful artifact they were supposed to protect actually has the power to control them, and they have to fight against its influence.
Well, in this fanfiction, perhaps the uncle has heard so much about the baby niece from the family. When they meet, he could be a bit nervous at first, but then as he holds her, he feels a deep connection and starts telling her stories about the family, even though she can't really understand yet.
He could meet his past allies in a different context. For instance, he might encounter Kakyoin or Polnareff when they were just starting their journey. Maybe he could also run into Dio at a time when Dio was still plotting his rise to power, which would create a very tense situation.
I don't know who Flower Sai is, nor do I have any information about the ending of her novel. If you provide more background information, I can try to provide you with a more accurate answer.
Perhaps his uncle has a very intimidating appearance or a loud voice that scares Harry. In the fanfiction, it could be that his uncle has a certain look in his eyes when he's angry that makes Harry tremble with fear.