It could be Sasuke. Imagine he goes on a long journey and comes back with a new name, having changed in some fundamental ways.
Naruto himself could be the main character. Maybe he has to take on a new name for some strategic reason during a big war and then comes back to the village with it. He would then have to deal with how the villagers react to his new identity.
Here's a more detailed plot. The character was thought to be dead but was actually in a different dimension. There, they were given a new name and a new purpose. When they come back to the Naruto world, they have to adapt to the changes that have occurred in their absence. They may have to team up with old friends and new allies to face a threat that is bigger than the village itself. They also struggle with whether to reveal their true identity or keep the new name as it represents a new start for them.
It could be a new villain who has emerged during Naruto's absence. This person might be after the power that Naruto holds or wants to destroy the Hidden Leaf Village for some unknown reason.
A young girl who has always been fascinated by the story of the Titanic could be the main character. She somehow finds herself transported back in time to the ship. She might be on a mission to save her favorite characters from the movie, like Jack. And through her journey, she discovers a lot about herself and the power of love and friendship on the doomed ship.
Madara Uchiha could also be a main antagonist. If Naruto goes back to a time when Madara was still alive and plotting, Madara would surely oppose Naruto's attempts to change the future. He has his own grand plans for the world and wouldn't let Naruto interfere easily.
Danzo could still be a major antagonist. Even if Naruto travels back in time, Danzo's thirst for power and his underhanded methods would still pose a threat. Naruto would have to find a way to deal with him without causing too much chaos in the village.
It could still be Naruto himself, just with a focus on a different, smaller part of his life or personality.
It could also be a young apprentice of the shopkeeper. This character could be learning the ropes of running the shop while also having dreams of becoming a great ninja. They would be in a position to interact with both the regular customers of the shop and the more famous ninjas, which could lead to all sorts of interesting storylines.
It could be Megaman himself. He could be transported to the Naruto world and have to adapt to the new environment while using his skills to make a difference. His sense of justice would fit well in the Naruto universe.
It could be an original character created specifically for the fanfiction. Maybe a rogue ninja with a vendetta against the Hidden Leaf Village.
Naruto himself could be the main character. Imagine Naruto getting his hands on a special pistol - like weapon and having to learn how to use it while still relying on his normal ninja skills. It would be a new challenge for him and could lead to some great character development as he tries to master this different form of combat.