The meeting could start with some misunderstandings. Naruto might mistake Jon Snow for an enemy at first due to his armor and sword. But once they realize they are not threats to each other, they could become fast friends. They could then decide to team up, with Naruto using his speed and Jon Snow his strength, to face any challenges that come their way in this fan - created world.
One scenario is that they meet on the battlefield. Jon is leading the North's forces, and Daenerys arrives with her dragons. At first, it seems like a confrontation, but then they realize they can be allies against a greater enemy. Another could be that Jon travels to Daenerys to seek her help. He bows before her, and she is intrigued by this northern lord. They start a conversation that leads to a partnership.
One common theme is the power dynamic. Jon is a respected leader in the North and Daenerys has her own power base in Essos. Their meeting often explores how they balance and combine their powers. Another theme is the discovery of their shared heritage. It usually leads to a deeper connection between them.
A meeting between them in fanfiction could be shown as a diplomatic encounter. Maybe Jon is sent back in time for some reason, and he has to negotiate with Aegon. He would use his wits and charm to make Aegon understand the future implications of his conquests. Aegon, being a shrewd leader, would listen intently and might even change some of his plans based on Jon's insights.
In many fanfictions, their meeting is a catalyst for change in the fight against the White Walkers. Jon Snow has first - hand knowledge of the threat, and Daenerys has the resources to combat it. Together, they are able to mobilize more forces and come up with better battle plans. Their union, whether it's a political or a romantic one, gives hope to the people of Westeros that they can be saved from the undead horde, which in turn shapes the rest of the fanfiction story.
Jon Snow could potentially have allies like the Mormonts. They have always been loyal to the Starks. Maybe even some of the Dornish houses might side with him. They have their own reasons to oppose the current power structure in Westeros. And of course, his friends from the Night's Watch who left with him or believe in his cause could be his allies in this conquest. He might also gain the support of some of the maesters who see the value in his leadership for the future of Westeros.
Daenerys Targaryen could be one to help. Since she has experience with dragons, she could give Jon Snow advice on how to care for the egg and hatch it.
It could be a young and untainted Frey. Maybe a niece or a cousin of the more infamous Freys. One who has not been involved in the past atrocities committed by her family and has a more noble heart.
Daenerys Targaryen is often paired with Jon Snow in such fanfictions. Their combined power and the potential for a different kind of relationship makes it a popular choice among writers. Another character is Arya Stark. Their sibling bond can be explored in new ways when Jon is reincarnated, like Arya helping Jon with her assassin skills in a different plot line.