Perhaps a villain in the fanfiction has the ability to manipulate both the powers of the Justice League's foes and Naruto's Mokuton. The heroes from both universes would have to team up. The Flash could use his speed to quickly move around the Mokuton - created forests, while Naruto and his friends could learn from the strategic minds of the Justice League like Wonder Woman.
One way could be through a crossover event where Naruto's Mokuton abilities are somehow transferred to a character in the Justice League universe. Maybe Batman discovers a way to harness Naruto's wood - style jutsu and uses it to combat a new threat in Gotham that is related to nature - based villains.
A plot could be that an ancient evil has awakened in both the Naruto world and the Justice League's world. This evil has the power to drain all life, similar to how Orochimaru drains chakra. The Mokuton, being a life - giving power, is seen as the key to stop it. The Justice League travels to the Naruto world to seek help from those with Mokuton abilities. Together, they train and develop new strategies to fight this common enemy.
Spider - Man's agility and web - slinging could be combined with Superman's flight. For example, Spider - Man could use his webs to attach to Superman while he's flying, allowing them to reach places faster. Or Batman could use Spider - Man's web - shooters in his utility belt for a new way to immobilize enemies. Flash and Spider - Man could work together to create a super - fast web - trap for villains.
Superman might feel a sense of guilt if he could have saved Naruto but didn't. He's always about saving lives, and Naruto's death would be a blow to his self - image. Batman would see it as a mystery to solve, trying to figure out how Naruto got to their world and what led to his death. Wonder Woman would be saddened by the loss of a potential ally. The Flash might be more cautious in future battles, seeing how quickly Naruto was taken down. Green Lantern could question his own power, as Naruto had unique abilities that he couldn't protect from.
Well, Naruto has his powerful ninjutsu. He could use his shadow clone jutsu to overwhelm the Justice League. With a large number of clones, he can create distractions and attacks from multiple directions. Also, his Rasengan is a very powerful attack that could cause significant damage to the members of the Justice League if they are not careful.
Well, if the fanfiction has a premise where Naruto has access to some sort of kryptonite - like substance (for Superman) and some anti - magic items (for characters like Zatanna if she's part of the JL). He could also use his ability to absorb and manipulate chakra to disrupt the energy fields of the JL members. For example, if he can disrupt the energy that powers up Flash's speed, he can slow him down and then defeat him. Then he can gradually take out the other members using his ninjutsu and combat skills.
The Kyuubi within Naruto represents a powerful and often uncontrollable force. In a crossover with the Justice League, this could be a source of both conflict and cooperation. The League might be wary of the Kyuubi's power, but Naruto's willpower to control it could earn their respect. They could work together to fight a common enemy that is drawn to the unique power that Naruto and the Kyuubi possess. Maybe an alien threat that wants to harness the Kyuubi's chakra for its own evil purposes. Naruto could use his Rasengan and other jutsu in combination with the League's powers, like Superman's strength or Batman's strategic mind, to defeat this enemy.
One way to combine them is through a crossover story. Imagine characters from My Hero Academia being transported to the Justice League's universe. For example, Deku could meet Superman and learn about a different kind of heroism. Their powers and ideologies could clash or complement each other. Another aspect could be the villains. The League of Villains could team up with some of the Justice League's foes, creating a huge threat that both groups of heroes have to face together.
Well, one possibility could be that Naruto's powerful ninjutsu skills give him an edge. He might use his Shadow Clone Jutsu to confuse the Joker and then land a fatal blow with a Rasengan. Another aspect could be Naruto's strong sense of justice which drives him to take out the chaotic Joker in the Justice League universe.
He might fit in by being a symbol of hope like Superman. Naruto has always been about protecting his village and the people he cares about. In the Justice League, he could extend that to protecting the whole world. His ability to make friends easily would also help him bond with the other members. For example, he could befriend The Flash and they could have races while also training together. And his Nine - Tails power could be a huge boost in battles against strong enemies.
Well, in a fanfiction, anything can be possible. Naruto's skills like his shadow clones and Rasengan could potentially be used to rescue Ace. Maybe he uses his speed to get through the Justice League's defenses, which are set up around Ace for some reason. And then he uses his clones to create a distraction while he frees Ace with his combat abilities.