One possible plot twist could be that Naruto discovers Godzilla is being controlled by an evil force. So instead of just fighting Godzilla, he has to find a way to break the control. Another could be that Godzilla is actually a guardian of some sort, and Naruto misinterprets its actions as aggression at first. Then they end up teaming up against a greater threat.
One possible plot twist could be that Danzo is actually being controlled by an even greater enemy. So, when Naruto is about to defeat him, he realizes that there's a bigger threat behind Danzo. Another could be that Danzo reveals a hidden power that he has been suppressing all along and suddenly becomes much stronger than Naruto expected.
One possible plot twist could be that Naruto discovers a way to nullify Jigen's power. Maybe he finds a weakness in the power source that Jigen draws from. Another twist could be that Jigen is actually being controlled by a greater evil, and Naruto has to figure out a way to free him rather than just defeat him. It could also be that Naruto loses his powers temporarily during the fight and has to rely on his wits and the help of his friends in unexpected ways.
One possible plot twist could be that Pikachu suddenly loses its ability to use electric attacks. This would completely change the dynamic of the battle as Pikachu would have to rely on physical attacks like Quick Attack, which might not be as effective against Bayleef. Another twist could be that Bayleef evolves during the battle into Meganium, gaining new and more powerful abilities that catch Pikachu off - guard.
One possible plot twist could be that the real enemy is secretly manipulating the Shinobi Alliance to fight Naruto. So Naruto has to not only defend himself but also figure out who is behind it all. Another could be that Naruto discovers a hidden power within himself during the fight that changes the course of the battle.
One interesting plot twist could be that Naruto is actually related to a Marvel character through some ancient connection. Maybe his chakra has a link to the Infinity Stones in the Marvel universe. Another could be that the Avengers are transported to the Naruto world and have to learn ninjutsu to survive. And a third one might be that Naruto gets the powers of a Marvel hero like Spider - Man and has to deal with the new abilities while still being a ninja.
Perhaps a plot twist would be that during the fight, Tai discovers a secret about Raven that completely changes his perception of her. For example, he finds out that she has been working undercover to stop a greater threat all along, and their fight then turns into a reluctant alliance against a common enemy.
Maybe the seventh swordsman has a secret power that is unleashed when Naruto is in a dire situation. This power could be something that was thought to be lost or forgotten in the Naruto world, and its appearance changes the entire dynamic of the story.
Maybe Naruto discovers that Matatabi has a hidden past that is linked to his own family. For example, his mother or father had a secret encounter with Matatabi before he was born, and this changes the way he views his family and his connection to Matatabi.
A plot twist could be that Naruto discovers a long - lost connection between the Nine - Tails and some ancient power in Kumo. This could change the whole dynamic of his capture situation. Instead of being a victim, he might become an important figure in Kumo's internal power struggle. And this new - found connection could also lead to a new alliance between Konoha and Kumo in the end. Another twist could be that Naruto's capture was a ruse by Konoha's higher - ups to gain some secret knowledge in Kumo. Naruto was sent there on purpose, but things start to go wrong when Kumo figures out the plan.
One possible plot twist could be that Naruto's closest friend turns out to be secretly working for the enemy. Just when Naruto is about to make a final stand against the invaders, his friend betrays him, leaving him in a difficult situation. But Naruto, being Naruto, manages to find a way to turn the situation around and still save the village.