Perhaps there is a powerful artifact. In Naruto's world, there are many powerful and mysterious artifacts. If one of these artifacts was activated, and it had some sort of connection to the Sonic universe, it could trigger a transformation. For example, an ancient scroll that was inscribed with both ninja magic and the energy signature of the Chaos Emeralds. When Naruto unrolled the scroll during a mission, the energy within it interacted with his chakra, resulting in his transformation into Shadow the Hedgehog.
Well, it could be due to a curse. There might exist a very ancient and powerful curse that was once sealed away. But through a series of events like tomb raiding by some evil forces, the curse was unleashed. Naruto, being in the wrong place at the wrong time, got affected by it and transformed into Shadow the Hedgehog.
Well, it could be that Naruto is exposed to a powerful and corrupting force. This force warps his sense of justice. Deadshot's character represents a more morally gray area compared to Naruto's traditional view of right and wrong. Maybe Naruto has a series of traumatic experiences that make him question his own values. He then sees Deadshot as a model of someone who can get things done regardless of the cost, and thus begins to transform into someone like Deadshot.
It could also be that a villain from the Shazam universe tries to take over Naruto's world. In the process, they create a situation where Naruto's chakra system gets infused with the magic of Shazam. This would be a really interesting development as Naruto would have to figure out how to use his new powers in a way that doesn't conflict with his ninja training. He might use his new - found flight ability to quickly get to different battle locations and his super strength to overpower enemies that were previously difficult to defeat.
Well, it could start with Naruto being exposed to some dark chakra that warps his mind, making him adopt Bane's ruthless and power - hungry ways. Maybe he loses all his friends in a tragic event and turns to Bane - like methods to gain enough power to prevent such a thing from ever happening again.
Well, one way could be through some sort of strange magical or scientific experiment. Maybe a rogue ninja or a mad scientist creates a device that accidentally fuses Naruto's chakra with Frieza's essence. This would start to change Naruto's physical and mental state, gradually making him more like Frieza.
Perhaps there's a powerful artifact in the Naruto world that has the ability to transform people into different superheroes from other universes. Naruto stumbles upon this artifact and, not knowing what it does, activates it and is transformed into Ant - Man. He then has to figure out how to use his new powers like shrinking, communicating with ants, and growing back to normal size while still being a ninja.
Another aspect could be in Naruto's leadership. As he grows older, he realizes the importance of Minato's calm and collected leadership in Konoha. Naruto might start to mimic Minato's diplomatic approach when dealing with other villages, just as Minato was respected for his ability to maintain peace and alliances. He could learn from Minato's past actions and start to handle village politics and international relations in a more Minato - like way.
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.
One possibility could be that Peter Parker, in a moment of extreme stress and anger, is exposed to the Carnage symbiote. Maybe he's facing a great loss, like the death of a loved one, and his emotions make him a prime target for the symbiote's takeover. The Carnage symbiote, known for latching onto negative emotions, might sense his turmoil and bond with him, thus leading to his transformation into a form influenced by Carnage.
Well, in fanfiction, anything is possible. Maybe Naruto gets transported to the Sekirei world through some sort of magic or a strange portal. This could be the start of his journey to become a Sekirei. It could also be due to a curse or a wish gone wrong that transforms him into a Sekirei - like form.
In a Naruto becomes a Terminator fanfiction, it could start with some sort of time - travel or interdimensional rift. Maybe a jutsu gone wrong sends Naruto to a world where the Terminator technology exists. Then, Naruto, with his ninja skills and strong will, might adapt to the new environment. He could use his chakra in unique ways combined with the advanced weaponry of the Terminator world.