Maybe a story where some of the younger members of the Young Justice team are frustrated with the Justice League's methods and decide to take on a mission on their own, but end up getting in over their heads and have to call in the League for help. This could lead to a lot of character development and some interesting dynamics between the two groups.
A fanfiction could explore the idea of a secret society within the Justice League that the Young Justice team discovers. The young heroes then have to decide whether to expose it or work with the League to reform it. This would involve a lot of mystery, intrigue, and moral dilemmas for the characters.
One idea could be a crossover where the Young Justice team has to team up with the Justice League to face an interdimensional threat. Maybe a powerful villain from another dimension is trying to invade Earth and the combined skills and powers of both groups are needed to stop it.
One idea could be that the Young Justice team gets accidentally transported to an alternate dimension where the Justice League has turned evil. The Young Justice members then have to figure out how to reverse the situation while also evading capture from their once - heroes. Another could be a time - travel plot where the Young Justice team travels back in time and teams up with the early days of the Justice League to stop a threat that was thought to be long gone but has resurfaced in their own time. A third idea is that a powerful new villain emerges who can only be defeated by a combined effort of the Young Justice and Justice League, but first they have to overcome their differences in fighting styles and leadership.
One idea could be a misunderstanding that leads to a battle. Maybe a villain manipulates the situation so that Young Justice thinks the Justice League has turned evil. For example, the villain uses mind - control technology on some of the League members and Young Justice has to fight to save them.
One idea could be a misunderstanding that leads to a fight. Maybe the Justice League mistakes some of Young Justice's actions as being too reckless and end up in a battle. Then they realize they were wrong when a real threat emerges and they have to work together.
One idea could be that the Young Justice team has to prove themselves to the Justice League during a major alien invasion. The League initially doubts their abilities but as the battle progresses, they see the unique skills and teamwork of the young heroes.
A cool plot could be a time - travel related crossover. The Young Justice team travels back in time and meets the younger versions of the Justice League members. They have to work together to stop a time - traveling villain from changing history in a way that would destroy the future. Or perhaps there's a magic - based crossover where a powerful sorcerer is causing chaos. The Justice League, which is more used to physical threats, has to team up with the Young Justice, some of whom have magic - related powers, to defeat the sorcerer.
One idea could be exploring the backstories of the lesser - known members in more depth. For example, you could focus on a character like Blue Beetle and his struggle to control the Scarab while also fitting into the team. Another idea is to create an alternate universe where the Justice League is evil and the Young Justice League has to oppose them. This would lead to some really intense battles and moral dilemmas for the young heroes.
A third interesting storyline might involve a secret alliance between a member of the Justice League and a villain that the Young Justice team discovers. This discovery then sets off a chain of events where the Young Justice team has to decide whether to trust the rest of the Justice League and how to handle this new information without causing a complete breakdown in the superhero community.
One idea could be that the Justice League members gain new gaming - related powers. For example, Superman could have the ability to instantly analyze any opponent's weaknesses like a game character stats screen. Batman could use his detective skills to hack into virtual reality systems within the story's universe.
One idea could be a story where Batman has to lead the Justice League in a fight against a new, powerful and mysterious villain that can manipulate time. Another could be a fanfiction exploring the relationships within the Justice League when they are stranded on an uninhabited planet and have to rely on each other more than ever.