Well, one possibility is that Naruto has some kind of premonition in the fanfiction. So he quickly rushes to Jiraiya's location where Pein is attacking. And he uses his shadow clones cleverly, distracting Pein long enough to rescue Jiraiya. He could also have some secret help from a new ally or an unexpected power boost from within himself.
In many fanfictions, Naruto's strong bond with Jiraiya might trigger some latent power. For example, his Nine - Tails chakra could mutate into a more powerful and controllable form. He might use this new form to fend off Pein's attacks. Also, Naruto could have been training in a special place that gives him the knowledge and skills to counter Pein's abilities specifically. He could then use these to not only save Jiraiya but also defeat Pein in a spectacular showdown.
In some fanfictions, Naruto might team up with other unexpected characters. Say, he teams up with some of the Akatsuki members who have a vendetta against Pein for some reason. Together, they are able to save Jiraiya from Pein's clutches.
It could be due to a curse. Maybe there is a long - forgotten curse placed on the Uzumaki clan, and Naruto accidentally triggers it. This curse slowly changes his nature and makes him more like Pein. His friends notice the changes but are initially powerless to stop it.
Well, Naruto could save Kushina from the Kyuubi in fanfiction through his strong willpower. We know Naruto has an unbreakable spirit. He might be able to communicate with the Kyuubi in a different way, like showing the Kyuubi a future where it doesn't have to be so violent. And by doing this, he could convince the Kyuubi to release Kushina. Also, Naruto might have received some special power or training that enables him to counter the Kyuubi's attack and save Kushina.
Well, one way could be that Naruto accidentally stumbles upon Itachi's plot against Mikoto. Maybe Naruto was in the right place at the right time, and using his ninja skills and his never - give - up attitude, he manages to fend off Itachi and save Mikoto. Naruto is known for his quick thinking in dangerous situations.
In such a fanfiction scenario, it could be due to a misunderstanding. Maybe there was false information spread about Naruto that made Jiraiya and Tsunade believe he had done something unforgivable. For example, an enemy could have framed him for a major crime against the village.
In this fanfiction scenario, Naruto could save Fairy Tail from Acnologia using his powerful jutsu. For example, his Rasengan or Sage Mode abilities might be enough to fend off Acnologia. Maybe he could also use his shadow clone jutsu to distract the dragon while Fairy Tail members prepare a counter - attack.
One way Naruto could save Whitebeard is if he somehow entered the One Piece world. Naruto is known for his strong sense of justice and determination. If he saw Whitebeard in danger, he would surely jump in to help. He could use his Sage Mode to enhance his strength and perception. With his enhanced abilities, he could sense incoming attacks on Whitebeard and intercept them in time. Also, his ability to communicate with others and form alliances quickly might also play a role in saving Whitebeard.
One way it could happen is if Naruto somehow gains the ability to travel back in time. Maybe through a powerful jutsu or a unique kekkei genkai. He could then use his knowledge of future events and his combat skills to save his parents from their tragic fate.
Well, Naruto is known for his determination. So in this 'Naruto saves Fuu from Akatsuki' fanfiction, he would likely draw on his experiences and the bonds he has with his friends. He might first try to negotiate with the Akatsuki, but when that fails, he'll engage in a fierce battle. He'll use his speed and agility, which he has developed over years of training, to dodge the attacks of the Akatsuki and rescue Fuu. And Fuu, on her part, might also have some unique abilities that could assist Naruto in their escape from the Akatsuki.
Perhaps the fanfic is exploring an alternate universe concept. In this universe, the relationship between Jiraiya and Naruto has been strained due to different events that didn't occur in the original story. Jiraiya's actions that seem like a betrayal could be a result of different political or personal circumstances in this alternate world. For instance, if there was a power struggle in the Hidden Leaf Village and Jiraiya sided with a different faction for some reason, Naruto would feel betrayed.