In a time travel fanfiction, their son could go back to the moment when Jon and Daenerys first met. He could subtly change their initial interactions to make them trust each other more quickly. This could lead to a stronger alliance from the start. He could also travel to the times when they faced their biggest challenges individually and offer solutions. For example, when Daenerys was dealing with the slavers in Slaver's Bay, he could give her ideas on how to end slavery more effectively and gain more loyal followers, which would have put her in a better position when she reached Westeros.
There's 'Time Traveling Dragons' which is an interesting take. They are sent back in time to a period where dragons were more common. Daenerys gets to see how her ancestors interacted with their dragons, and Jon is there to support her. The story has a lot of twists and turns as they try to find a way back to their own time while also changing some things in the past for the better.
One idea could be that they travel back to the time when the Targaryen dynasty was at its peak. Jon could see Daenerys in her element as a Targaryen princess. They might try to change some of the events that led to the downfall of the Targaryens, like preventing the Mad King's actions. But this could have unforeseen consequences for the future they came from.
It would greatly affect Jon. If their son travels back to the time when Jon was still at the Wall, he could reveal to Jon his true identity earlier and help him accept his Targaryen heritage more smoothly. This could change Jon's actions and decisions. For Daenerys, the son could give her more confidence in her claim to the Iron Throne by showing her the future support she could have had.
One interesting storyline could be their journey together after uniting their forces. Maybe they face a new, unexpected threat that tests their relationship and leadership. Another could be a story where they have to navigate the political intrigue of Westeros together while also dealing with their growing feelings for each other.
One possible plot could be that Harry travels back in time to Tom Riddle's school days at Hogwarts. He could try to prevent Riddle from turning into Voldemort by befriending him and showing him a different path. Maybe Harry uses his knowledge of the future to expose the dark magic that was influencing Riddle at the time.
One possible plot could be that James, Lily, and Albus travel back in time to the Marauder's era. They could interact with the young versions of their family members, like Sirius and Remus. Maybe they try to change some small events to prevent future tragedies without messing up the timeline too much.
Another plot could involve them traveling to a different timeline altogether. In this new timeline, they might find themselves in a world where the power of Geass doesn't exist. This would force them to rely on their wits and leadership skills in a completely different way. They could either try to find a way back to their original timeline or decide to make the best of the situation and change this new world for the better.
One possible plot could be Future Trunks traveling back in time to prevent a new threat that he discovers in his own time. For example, a powerful and unknown enemy is about to emerge in his future, and he goes back to enlist the help of Goku and the others before it's too late. Another plot could involve Trunks accidentally changing something in the past that has unforeseen consequences in his future, like messing with the timeline of a certain character's power - up, which then leads to a whole new set of challenges when he returns to his own time.
Another plot could involve Starkiller traveling to the time of the Old Republic. He could interact with the ancient Jedi and Sith, learning their ways and perhaps even influencing the development of the Force teachings. Maybe he discovers a long - lost Force technique that changes his perspective on the Force and his own powers.
Another plot could be that they meet under very different circumstances. For example, Jon is sent as an emissary to Daenerys much earlier in the story. At first, Daenerys is skeptical of Jon's claim to the North and his intentions. However, as they spend time together, they discover a shared history of their families and a mutual desire to make Westeros a better place. This discovery leads to a strong bond between them, and they start planning strategies to reshape the political and power landscape of Westeros together.