Perhaps a story where they all have to deal with a new villain who has the ability to nullify their powers temporarily. They are forced to work together in a more covert way. Batman uses his gadgets, Superman his knowledge of science (since he can't use his strength), and Wonder Woman her wisdom and leadership to outwit the villain.
One plot idea could be a team - up where they face a new, extremely powerful villain that neither of them can defeat alone. This villain could have powers that are a combination of their weaknesses, like a being that can manipulate kryptonite and also has the strategic mind of Batman's enemies. They would have to learn to work together in a new way.
One great Superman, Wonder Woman and Batman fanfiction is 'The Trinity Alliance'. It shows them working together against a powerful new villain. The story does a great job of portraying their unique powers and personalities. It has some really cool action scenes where Superman's strength, Wonder Woman's combat skills and Batman's strategic mind all come into play.
One plot idea could be that an otherworldly threat emerges that only their combined powers can stop. They have to put aside their differences and work together seamlessly. For example, a powerful alien race plans to invade Earth and they need to use Batman's strategic mind, Superman's super strength and Wonder Woman's combat skills.
A popular type of Wonder Woman and Batman fanfiction is the alternate universe ones. For example, a story where they are in a world where all the superheroes' powers are reversed. Batman might have some kind of super strength while Wonder Woman has to rely more on her gadgets and detective skills like Batman usually does. These types of stories are interesting as they allow the writers to explore different aspects of the characters that we don't usually see in the main canon.
The idea of love triangles or complex romantic relationships within the Trinity is also a theme. Some fanfictions explore the possibility of romantic feelings between Batman and Wonder Woman, or Superman and Wonder Woman, and how that would affect their dynamic as a team and their individual characters.
One popular theme is the team - up. Writers like to explore how Superman, Batman and Wonder Woman work together to fight a common enemy. It shows their different powers and personalities interacting.
One popular theme is the love triangle between Superman, Wonder Woman and Batman. Writers often explore the complex relationships that could develop among them. Another theme is them teaming up against a powerful enemy that none of them could defeat alone. This shows their combined strength and the importance of their alliance in the DC universe.
One common theme is the team - up. Writers often explore how Batman, Superman, and Wonder Woman work together to face a powerful enemy. It could be a new super - villain or an old foe with a new twist.
There are fanfictions where Batman and Wonder Woman meet in an alternate universe. For instance, in a world where all the superheroes have different powers. In this fanfic, Batman could have some sort of magic - influenced by Wonder Woman's own mythological background - and Wonder Woman might have a more detective - like approach. They meet when trying to solve a crime that seems to be beyond the capabilities of the other superheroes in this universe. Their combined skills and different perspectives make for an exciting story.
One great storyline could be Batman and Wonder Woman teaming up to face a new, powerful villain in the JLU universe created by a fanfic writer. Maybe a villain who can manipulate time, forcing them to rely on each other's unique skills. Batman's detective skills and strategic mind combined with Wonder Woman's combat prowess and divine powers would make for an exciting adventure.