In a lot of fanfics, Naruto is stronger than Sasuke. Naruto has always had an incredible willpower and in fanfics, this can be translated into him achieving greater power levels. His ability to make friends and allies can also lead to him getting more support and resources in the story. For example, he might get some special training from an ancient sage that Sasuke doesn't have access to. Also, his positive attitude can attract more powerful beings to help him out, which gives him an edge over Sasuke in terms of strength.
Well, one way could be in their physical abilities. Maybe in the fanfic, Naruto is shown to have some of Zetsu's stealthy movement skills, like being able to blend into the environment in a similar way. Another similarity could be in their connection to nature. Zetsu has a strong link to the plant - like aspects of nature, and Naruto's chakra might be shown to have a similar kind of connection in the fanfic.
Naruto is stronger in fanfiction because of his ability to connect with others. He has made friends all over the ninja world. This network of friends often provides him with support in battles, whether it's intel or actual combat help. Also, his training under Jiraiya was very comprehensive. Jiraiya taught him not only combat skills but also how to be a better person. This made Naruto grow both physically and mentally. And compared to Sasuke, Naruto seems to be more adaptable to different fighting styles in fanfiction, which gives him an edge in combat.
One reason is that Naruto has the Nine - Tails' chakra. In fanfic, this power can be further enhanced or manipulated in ways that make him far more powerful than Sasuke. Another reason could be his more outgoing personality. He might be able to form alliances more easily, leading to him having more resources and power - ups at his disposal.
There are fanfictions where Naruto, using his Uzumaki clan's sealing techniques along with his chakra, is able to break through Sasuke's genjutsu. Genjutsu is one of Sasuke's strong points usually, but Naruto's unique abilities give him the upper hand. Also, in certain stories, Naruto's connection to the nature energy in his Sage Mode is so strong that he can heal himself during a fight with Sasuke, while Sasuke doesn't have such a convenient self - healing ability.
I'm not sure specifically as there could be many different interpretations in fanfiction. But it might involve Zetsu using his unique abilities to rescue Naruto from a dangerous situation, like a powerful enemy attack or a life - threatening trap.
Another plotline might be Naruto's strength leading to a different kind of peace in the ninja world. Since he's stronger, he can enforce his ideals more effectively. He could start a new era of cooperation among the ninja villages by using his power to make the other villages see the benefits of unity, and Sasuke might be reluctantly following his lead.
In a fanfic where Naruto is trained by Zetsu, the story could take an interesting turn. Zetsu has knowledge of the Akatsuki and their secrets. Naruto could learn about the organization from the inside out. This knowledge could help him in his quest to bring peace. He might also gain some physical enhancements. Zetsu is quite durable in his own way, and Naruto could inherit some of that sturdiness. This would make him an even more formidable opponent in battles against strong foes like Pain or Madara.