For a Naruto Kyuubi and Justice League fanfiction, a great plot could be that an ancient evil from the Naruto universe that was sealed away by the Kyuubi's power long ago is released in the DC universe. Naruto, with the help of the Justice League, has to track it down and reseal it. Along the way, he and the League members learn from each other. The Flash could learn about Naruto's chakra - enhanced speed, and Naruto could learn about the Flash's use of the Speed Force. Batman could analyze Naruto's fighting style and help him improve it, while Naruto could show Batman some ninja - inspired stealth and infiltration techniques. There could also be a cultural exchange as Naruto tries to understand the modern world of the Justice League and they try to understand the feudal - like society of the Naruto world.
A really interesting plot idea would be if the Kyuubi's chakra somehow gets corrupted and Naruto starts to lose control. The Justice League has to help him regain his sanity and control over the Kyuubi. Also, a plot where the Justice League and Naruto with the Kyuubi team up to take on a powerful interdimensional being that is causing trouble in both their universes. They have to combine their different powers and strategies to win. And perhaps, there could be a sub - plot where Naruto tries to understand the different values and ethics of the Justice League members compared to his own ninja world.
One interesting plot idea is the exchange of powers. For instance, if Batman were to somehow gain the ability to use Fairy Tail magic, it would completely change his combat and detective approach. He could use magic spells to enhance his gadgets or solve mysteries in a more magical way.
One plot idea could be the Justice League members learning Naruto's ninja techniques. They could incorporate these into their crime - fighting, while the harem aspect adds a layer of relationship drama and support among the characters.
One idea could be Naruto somehow getting transported to the DC universe and joining the Justice League. He could use his ninja skills, like shadow clones, to confuse villains during battles. For example, when facing a powerful foe like Darkseid, Naruto's clones could swarm him, making it hard for him to target the real Naruto.
One plot idea could be that Naruto is somehow transported to the Justice League universe. He meets various female heroes and they are intrigued by his unique abilities and his strong sense of justice. For example, he could team up with Wonder Woman and they start to develop a mutual respect that slowly turns into more. Another could be that a villain uses a spell to make all the female Justice League members attracted to Naruto at the same time, leading to a chaotic and comical situation as he tries to figure out how to handle it without causing rifts in the team.
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.
A darker plot idea could involve a powerful villain who has somehow found a way to corrupt both universes. This villain uses the technology and powers from both My Hero Academia and the Justice League's worlds to create a doomsday scenario. The heroes must put aside their differences and combine their strengths to stop this new threat. This would involve a lot of character development as they learn from each other's methods of heroism and sacrifice.
The idea of the Akatsuki joining forces with some of the villains in the DC universe is also quite fascinating. It creates a huge chaos as the combined forces of the ninja villains and the super - villains from DC pose a great threat. And then it's up to Naruto and the Justice League to stop them. There are many intense battles and interesting character dynamics in such crossovers.
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.