A fanfiction could explore the backstory of some of the side characters in both games. For instance, in Twilight Princess, you could write about the life of Midna before she got involved with Link. Or in Skyward Sword, you could delve into the past of Groose and how his relationship with Link developed over time. This could add more depth to the overall Zelda universe in the fanfiction.
For Skyward Sword fanfiction, you could write a story about the different races in the game. How they interact with each other, their cultures, and traditions. For instance, you could write about a young Goron who wants to learn about the Loftwings and travels to Skyloft. Or a story about a Zora who has a special connection with the Goddess Statue and tries to protect it from the forces of evil. There are many possibilities when it comes to exploring the races in the game.
One idea could be that the princess has a secret power that is awakened by the Twilight world. Maybe she can communicate with the Twilight creatures and they help her solve a mystery in her own kingdom.
A great plot for a Twilight Princess story fanfiction could be a time - travel aspect. Link somehow gets sent back in time to a point before the Twilight invasion. He could then try to prevent it from happening in the first place. This would involve him interacting with characters in a different way, and he might have to make some tough decisions about changing the future.
One interesting plot idea could be exploring how different characters adapt to the post - apocalyptic world in new and unexpected ways. For example, a character who was once a timid office worker becomes a fearless scavenger.
Focus on unique character interactions. Instead of just following the typical relationships shown in the games, create new dynamics. For example, make Zelda from Twilight Princess have a more confrontational relationship with the Skyward Sword Link at first, and then gradually develop a deep friendship as they face challenges together.
One idea could be Link and Ilia going on a secret adventure to discover a hidden magic within the Twilight Realm. Maybe they find an ancient artifact that has the power to restore a part of the Twilight Realm that was damaged. Another could be a story where Ilia gets kidnapped by an unknown enemy and Link has to go through a series of difficult trials to rescue her. He could face new and dangerous creatures along the way.
One idea could be exploring Midna's backstory in more detail. Maybe how she came to be in the Twilight Realm and her relationships there before meeting Link. Another could be a story where Link has to face a new, previously unknown enemy in the Twilight Realm that is even more powerful than Zant. For example, an ancient evil that was sealed away long ago but is now starting to break free.
A plot could involve a new vampire in the Twilight universe who is ashamed of their transformation and uses a mask to try and fit into human society again. They struggle with their new instincts while trying to keep their identity a secret. Along the way, they meet other characters from the Twilight series and their story unfolds in a way that challenges the norms of the original story.
One idea could be a new vampire character being reborn in the Twilight universe with a special power, like the ability to control the weather. This would create a whole new dynamic as they interact with the Cullens and other vampires.
One idea could be exploring a new magical creature in the Twilight universe. For example, a magical being that can control time and how it affects the relationships between vampires, werewolves and humans. Another plot could involve a character from the Twilight world getting lost in a different magical realm and having to find their way back, all while facing new and strange challenges.