It could be an epic battle. Maybe they have a misunderstanding or are forced into a fight by external circumstances.
The idea of destiny is a big one. Writers like to play with the concept of whether Jon is truly meant to be a hero or a king. His journey to fulfill what might be his pre - ordained fate is a theme that recurs often in Jon Snow fan fiction. It gives a sense of grandeur and purpose to his character.
One common theme is the union of the North and the South. Jon represents the North and Daenerys the South in a way. Their coming together is seen as a way to unite the different regions of Westeros against common threats.
In this fan fiction, their relationship may develop in a complex way. Stannis may initially use Jon as a tool to gain more support in the North, seeing his Stark name as an advantage. But as Jon shows his true self and his unique skills, Stannis starts to value him for who he is. Jon, on the other hand, may be initially hesitant about serving Stannis but gradually realizes that he can learn a great deal from him. Their relationship could be full of power struggles, but also moments of mutual admiration and growth.
The plot could involve a power struggle. Aegon wants to reclaim the Iron Throne for the Targaryens. Jon, on the other hand, has his own loyalties. They could start as rivals. But then, when a new threat emerges, like a powerful dark magic user who wants to rule Westeros through chaos. They are forced to put aside their differences. Jon's knowledge of the North and Aegon's Targaryen heritage could be combined to fight this new foe.
In a fan fiction, they might discover that they are related in a more complex way than they thought. Maybe they find out that there is a hidden prophecy that requires both of their bloodlines to come together to bring peace to Westeros. This could lead to a journey where they travel together, facing various challenges and gradually building a bond of friendship and respect.
One possible storyline could be Jon Snow learning the ways of leadership from Stannis. Stannis, being a strict and experienced leader, could teach Jon about military strategies and the importance of justice. Jon, in turn, might influence Stannis with his more empathetic and inclusive approach, leading to a change in Stannis' view towards the Free Folk.
One that stands out is 'Jon Snow's Redemption'. It's set after the events of the show and imagines a path of redemption for Jon. It shows his struggle with his identity and his attempts to make amends for past actions. It's quite a thought - provoking read.
One interesting plotline could be them uniting the kingdoms without the bloodshed that occurred in the show. They might use their combined influence and the respect people have for them to bring about peace. For example, Jon's connection to the North and the wildlings, along with Daenerys' army and dragons, could be used to defend all of Westeros against a common enemy like the White Walkers that they both faced in different ways in the original story.
There's a fan fiction called 'When Jon Met Dany'. This one is unique as it starts from the very beginning of their encounter and builds up their relationship in a very detailed way. It shows their initial doubts about each other slowly turning into trust and then love. And 'Jon and Dany: United for Eternity' is a fan fic that imagines a world where they are able to create a long - lasting peace in Westeros together, with their relationship at the center of it all.
One popular type is where they meet earlier in their journeys and form an alliance much sooner. In these fictions, their combined forces often change the political landscape of Westeros in unexpected ways. For example, they might be able to take King's Landing without as much bloodshed as in the original series.