Maybe Naruto's godlike abilities are a result of some dark force that the village doesn't understand. They think he's been corrupted by it, so they banish him. As he's banished, he could start a journey of self - discovery, trying to figure out what happened to him and how to control these new powers. He might also encounter other outcasts who help him see the situation in a new light.
One possibility is that Naruto's new 'godlike' powers after the Pain arc are seen as a threat by the village elders. They fear he might become uncontrollable, so they banish him. This could lead to Naruto exploring new lands, meeting new allies or enemies, and potentially finding a way to prove his worth and return.
One possible plot could be that Naruto is wrongly accused of something after the Pein attack. Maybe the village leaders believe false rumors that Naruto was in cahoots with Pein somehow. As a result, he is banished. He then goes on a journey to prove his innocence and in the process, he discovers new powers and allies. He might also encounter some of Pein's former followers who have their own motives and secrets related to what really happened during the attack.
It could be the village elders. Since they banish Naruto, they could continue to be the main obstacle in his path. They might try to prevent him from coming back or try to eliminate him if they think he's a threat to their power and the village's stability.
It could be Danzo. He has always been suspicious of Naruto and might see this as an opportunity to get rid of him for good. He could spread false information to make the village turn against Naruto after the Pein attack.
In this 'godlike Naruto banished by parents' fanfiction, the plot might start with Naruto showing extraordinary abilities that are far beyond what his parents expected. They banish him out of fear for the balance of the ninja world. Naruto, being banished, might go into hiding in a far - off land. There, he could train even more rigorously to master his powers. He may also encounter other outcasts who have their own stories. Eventually, he might decide to return to his village to either seek revenge or to show his parents that he can use his powers for good.
Maybe Naruto's connection to Pein through the Nine - Tails is misinterpreted. Since Pein was after the Nine - Tails, the village believes Naruto is a liability. Banished, Naruto wanders into a hidden land where he learns ancient ninja techniques that are far more powerful than what he knew. He could then return to the village as a changed and more powerful ninja, but with a sense of bitterness towards those who banished him.
One possible plot could be that the other villages fear Naruto's power after the war. They put pressure on the Hidden Leaf to banish him. Naruto, feeling betrayed, leaves but then starts to discover new powers or allies in his exile as he tries to prove his worth and find a way back home.
Naruto might start to question his own identity. Being banished makes him feel like he doesn't belong anywhere. He could then start to explore his Namikaze heritage more deeply. He might discover secrets about his father that were hidden from him, and this knowledge could give him new strength and purpose. He could also use this newfound understanding to try and redeem himself in the eyes of the Hidden Leaf.
He could find a new home. For example, he might stumble upon a hidden village that accepts him for who he is and his powerful bloodline. There, he could train and become even stronger.
In the fanfiction, Naruto could also develop new strategies for fighting. Pein is a strategic mastermind, and under his training, Naruto might learn how to better analyze his opponents, anticipate their moves, and come up with more effective battle plans. This could give him an edge in future battles against powerful enemies.
Naruto could also become determined. Since he is 'godlike' in this fanfiction, he might see this as an opportunity to grow even stronger away from the village. He might set out on a journey to master his powers fully and prove himself, with the intention of one day coming back to the village and showing everyone that he was wrongly banished.