One possible way is through some sort of powerful jutsu gone wrong. Maybe a forbidden jutsu that was meant to do one thing but instead warped Naruto's being and made him take on the form and some of the characteristics of Madara Uchiha. It could also be the result of some dark magic or curse that was placed on him by an enemy who wanted to disrupt the balance in the ninja world.
Perhaps there is a time - travel element involved. Naruto could be sent back in time and somehow end up merging with Madara Uchiha's essence. This could be due to a malfunction in a time - travel device or a miscalculation by a powerful time - traveling ninja. As a result, Naruto's mind and body start to change and he begins to exhibit traits of Madara.
Well, it could be due to some dark influence. Maybe Orochimaru gets his hands on some ancient jutsu that can corrupt Naruto's mind and make him adopt Madara's ruthless ways. For example, if Orochimaru manages to tap into the same power source that once drove Madara to seek power at all costs.
If Naruto becomes Madara Uchiha in fanfiction, it could drastically change the plot. Firstly, the relationships would be turned upside down. Naruto's friends might see him as an enemy, especially Sasuke who has a complex relationship with the Uchiha legacy. The power dynamics in the ninja world would also shift. Naruto, with Madara's power and knowledge, could either rule with an iron fist or try to reshape the world in a more extreme way compared to his original goal of peace. And the Akatsuki's plans would likely be disrupted as Naruto, in Madara's form, might have different motives regarding the tailed beasts.
One possible way the storyline could develop is that Naruto would inherit some of Madara's powerful Uchiha abilities, like the Sharingan or even the Rinnegan. This would completely change his power dynamics in the ninja world. He might also face different challenges and enemies, as there could be those who fear his newfound power or connection to Madara.
If Naruto were to become like Madara in fanfiction, it would be a huge shift. Naruto has always been about hope and friendship. But like Madara, he could start to see the ninja world as something that needs to be reshaped by his own hands, regardless of the cost. He may abandon his village's values and try to impose his own version of order. This would lead to conflicts with his former allies. For example, Sasuke might be one of the first to oppose him as Sasuke has his own ideas about the ninja world and would not easily accept Naruto's new Madara - like ways.
There would be a power shift. Since Madara was extremely powerful, Naruto - as - Madara would be an almost unstoppable force. Other villages would have to either ally with Konoha (which would be a difficult decision considering the situation) or try to find a way to counter this new threat. This could lead to a new arms race among the ninja villages.
One way the story could develop is that Naruto would have an innate understanding of powerful Uchiha techniques. Since Madara was a master of the Sharingan and had many powerful jutsu. Naruto might be able to quickly master the Sharingan if he inherits it. For example, he could use it to enhance his combat abilities against stronger enemies. He could also have a different relationship with Sasuke. Maybe instead of being rivals, they could be more like cousins with a shared heritage to explore.
In fanfiction, the author could create a scenario where there was a secret relationship between an Uzumaki ancestor of Naruto and an Uchiha. This relationship could have been hidden for generations. And through some family secrets being revealed, it's discovered that Naruto is actually Madara's grandson. It could also involve some kind of genetic manipulation or curse that ties the two families together in a way that wasn't known before.
One way this could happen is through some sort of interdimensional rift. Maybe a powerful jutsu in the Naruto universe accidentally tears open a portal to the Star Wars galaxy. Naruto, being the curious and brave ninja he is, gets sucked into it. Once in the Star Wars universe, he's exposed to the dark side of the Force, which gradually corrupts him and he starts to take on the persona of Darth Vader. He might even learn some of the Sith ways from Vader's own teachings if he somehow travels back in time to Vader's era.
In this fanfic, Naruto could finally gain the respect he truly deserves as a Jounin. He might lead his own team and pass on the lessons he learned from Kakashi and others. His unique jutsu like the Rasengan could be further developed and he could use it in more creative ways during missions.
In such a fanfic, Naruto could have a very different appearance. He might have the dark hair typical of the Uchiha, and his eyes could be a unique blend of his Uzumaki and Uchiha heritage. His fighting style could also change, incorporating more Uchiha - style jutsu. For example, he could be more proficient in fire - style jutsu, which was common among the Uchiha.