A possible fanfiction could involve Naruto being a wildcard in the Civil War. He doesn't really understand the full politics of the situation at first. But as he learns about the registration act, he decides to oppose it. He teams up with some of the anti - registration superheroes and uses his unique abilities like chakra control and rasengan to fight against those who want to enforce the act.
The Naruto civil war in the Marvel fanfiction would likely introduce new power sets and abilities. The Marvel heroes and villains would be exposed to things like chakra manipulation and unique jutsu. This could inspire some of them to develop new ways to fight or gain power. For instance, Loki might try to use the power of the tailed beasts for his own nefarious purposes. It would also create a new source of conflict as different characters in the Marvel world would have different opinions on how to deal with the Naruto civil war.
One possibility is that the shinobi skills from Naruto could be pitted against the superpowers in the Marvel world. For example, Naruto's clones might be used to confuse and outmaneuver the likes of Spider - Man. Or perhaps the Sharingan could be used to predict the moves of characters like Captain America. It would be a chaotic and exciting crossover.
A common plot idea is time travel. The heroes could go back in time to before the events that led to the Civil War and prevent them from happening. For instance, they could stop the creation of the Sokovia Accords or resolve the issues that made the heroes split in the first place.
One idea could be that a new hero emerges during the Civil War and tries to find a middle ground between the two factions. They might have unique powers that allow them to communicate with both sides on a deeper level, and they end up uniting some of the heroes against a common, unexpected threat that was using the Civil War as a distraction.
Naruto's shadow clone jutsu could tip the balance. If he sides with one of the factions, he can create a large number of clones to overwhelm the opponents. For instance, if he's with Captain America's side, the clones can be used for reconnaissance and in battles, making it harder for Iron Man's side to predict their moves.
One idea could be that Peter Parker decides to unmask himself as a political statement during the Civil War. He might feel that the secrecy in the superhero community is causing more harm than good and by unmasking, he hopes to start a new era of transparency among heroes.
One idea could be a secret alliance within the superfamily. For example, two members who seem to be on opposite sides during the civil war are actually working together to expose a greater threat that has been fueling the conflict. This would add an element of mystery and change the dynamics of the war.
In Marvel Civil War main story, it's basically a big rift among the superhero community. Iron Man's side thinks registration is necessary as superhero actions can cause a lot of destruction. Captain America, on the other hand, feels that the government might misuse the registered superheroes. There are battles between the two factions, friendships are broken, and it's a huge chaotic situation that shakes the Marvel universe.
Some notable characters died, like Goliath. But the deaths had a significant impact on the story and the Marvel universe.
In the Marvel Civil War comics, there's no straightforward single winner. Both sides have their moments and losses, and it's more about the complex consequences and changes it brings to the Marvel universe.