A great plot for Young Justice Invasion fanfiction might be to have the team deal with internal conflicts during the invasion. Maybe there are trust issues among some members because of secrets that come to light. For example, if a member was unknowingly related to one of the invaders. This would create drama and force the team to work through their issues while also fighting the external threat. Also, you could explore how the invasion affects the public perception of the young heroes. Are they seen as saviors or are people scared of them bringing more danger?
One idea could be Naruto being transported to the Young Justice universe during the Invasion arc. He could use his unique jutsu skills like the Rasengan to fight off the invaders. Maybe he teams up with the Young Justice team and teaches them some of his ninja techniques.
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 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 exploring a new villain that the team has to face. This villain could have powers that are the opposite of the combined powers of the Young Justice team. For example, if the team has powers related to light and energy, the villain could have powers of darkness and entropy. Another plot could be a time - travel story where a member of the team goes back in time and accidentally changes something that has a huge impact on the present. Maybe they prevent a key event that led to the formation of the team, and they have to figure out how to fix it.
One idea could be exploring a new villain from a different dimension who has powers that disrupt the team's usual strategies. Another could be delving into the backstories of some of the lesser - known characters in the Young Justice universe and how they got their powers. Maybe a plot where the team has to deal with a powerful magical artifact that is corrupting the minds of the civilians.
Another plot could involve a new threat emerging that is related to the events of Endgame. The team has to piece together clues from the past events to stop this new danger. They might discover secrets that were hidden during Endgame that could change everything.
One idea could be a Young Justice member getting bitten and turning into a werewolf and having to hide it from the team at first. Another is a werewolf - based villain that the team has to face, who has some connection to an ancient werewolf legend in the DC universe. Maybe a story where a werewolf is used as a weapon by an evil organization against the Young Justice team.