Well, perhaps in this fanfiction, Evil Minato and Kushina find Naruto when he is at a very vulnerable state. They see an opportunity to use him for their evil plans. Their plans might involve using Naruto's Jinchuriki power to open a portal to a dimension full of dark energy. But Naruto, being the resilient character he is, tries to resist them. He calls upon the memories of his friends and the village that has always supported him, and he gradually starts to turn the tables on his 'evil' parents.
In this fanfiction, Evil Minato and Kushina find Naruto because they believe he holds the key to a powerful artifact. They think that by getting Naruto, they can obtain this artifact and rule the ninja world. However, as they get closer to Naruto, they start to notice his kind heart and the love he has for the village. This makes them recall their own past love for Konoha. Slowly, they begin to have second thoughts about their evil actions and consider changing their ways.
One possibility could be that Naruto discovers a long - hidden secret about his family that makes him feel betrayed. For example, he might find out that Minato and Kushina had made a deal with a dangerous enemy in the past that put the village at risk. This would be so against Naruto's values of protecting the village and his friends that he decides to leave them.
Maybe in the fanfiction, there is a powerful enemy who wants to use Naruto's connection to his parents against him. So, they somehow manage to bring Minato and Kushina back to the physical world. When they meet Naruto, it's an emotional moment. They form a plan to defeat the enemy together. Minato uses his strategic skills, Kushina her strength, and Naruto his own unique abilities learned over the years.
Perhaps in this fanfiction, Minato and Kushina leave Naruto because they are cursed. They fear that the curse will harm Naruto if they stay close. So, they go into exile. As Naruto grows up, he starts to discover clues about his parents' real reason for leaving and sets out on a quest to find them and break the curse. This could lead to many adventures and character - development moments for Naruto.
One possible fanfiction could be where 'evil Minato and Kushina' are under some sort of dark magic or mind control. They find Naruto not as their beloved son but as a target. Maybe they are being manipulated by a powerful enemy of the village who wants to use Naruto's power for evil. However, Naruto's pure heart and the bonds he has formed with his friends start to break through the false personas of his parents.
One possible plot could be that with Minato and Kushina alive, Naruto grows up in a complete family. They could train Naruto together, passing on their unique jutsu. Maybe Minato could finally fulfill his dream of bringing long - lasting peace to the Hidden Leaf with his family by his side. And Naruto would have a different kind of confidence and growth, not having to face the loneliness he did in the original story.
One possible plot twist could be that Naruto, instead of seeking acceptance in the village, decides to leave and find his own path outside. He might discover a hidden group or power that the village was unaware of and use it to come back and prove himself to his parents. Another twist could be that Naruto is taken in by an enemy of the village who sees his potential and trains him to be a powerful ninja, but for their own evil purposes. However, Naruto, having been ignored by his parents, might be more susceptible to this false sense of belonging.
Well, perhaps the plot could involve Minato having a secret evil plan all along. He could have used Naruto as part of this plan without Naruto knowing. Naruto then starts to notice strange things related to his father. As he digs deeper, he finds out about Minato's true nature. This could lead to Naruto having to choose between following in his father's footsteps (for some strange reason like power) or defying him and becoming a true hero on his own terms. The story could also involve Naruto's friends either turning against him because of his relation to Minato or helping him to overcome this difficult situation.
One possible plot twist could be that with Minato and Kushina alive, Naruto's training would be completely different. Minato, being a prodigy, could teach Naruto advanced jutsu much earlier. And Kushina might pass on some unique Uzumaki clan techniques. Maybe they would also change the political situation in Konoha, as Minato was a highly respected Hokage. This could lead to different alliances and power dynamics within the village and among the other ninja villages.
It might be due to jealousy. If Minato was getting more attention or praise in the village for his achievements while Kushina felt overlooked, that could create resentment. Say, Minato was constantly being hailed as a hero for his speed and battle tactics, and Kushina, who also had great power, felt like she was in his shadow.
A plot twist could be that they see Naruto losing his way. This would be a huge shock for them as they always believed in Naruto's goodness. But then, as the story unfolds, Naruto finds his way back due to a memory or a message from his parents that he somehow receives in a moment of crisis.