A possible plot could be a time - travel related one. A character from the Regeneration world accidentally travels to the Young Justice timeline and messes up some key events. Now the Young Justice team, along with the help of some friendly Regeneration characters, have to fix the timeline while also dealing with the consequences of the changes that have already occurred.
One idea could be that Naruto is somehow transported to the Young Justice universe. He then has to learn how to work with the team while also dealing with villains he's never faced before. Another plot could be that a villain uses some sort of magic or technology to merge the two worlds, forcing Naruto and the Young Justice members to cooperate to separate them again.
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.
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.
One idea could be that Ghost Rider somehow gets transported into the Young Justice universe. He might initially be seen as a threat by the team. But then they realize he's fighting against a common evil that has ties to the dark forces in both their worlds. For example, a demon that is trying to open a portal to bring more chaos.
Another idea is that the OC is a non - magic user who gets caught in a magical conflict that Zatanna is involved in. The OC has to rely on their wits and physical skills while Zatanna uses her magic. Their relationship could grow as they learn from each other's strengths and weaknesses. For example, the OC might teach Zatanna some street - smart tactics, and Zatanna could introduce the OC to the world of magic.
One idea could be exploring how the Young Justice team would react to the dystopian world of Injustice. For example, they might try to find a way to restore justice and balance without using the extreme methods seen in the Injustice universe. Maybe they would focus on rehabilitating the villains instead of just punishing them.
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.
From the Regeneration side, if there is a character with some sort of energy - based powers, they could be a good focus. Paired with Robin from Young Justice, they could create some really interesting strategies in battles. Another option could be a character who has a strong moral code from Regeneration, and when put together with Aqualad from Young Justice, they could have some great discussions about leadership and responsibility.