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.
One possibility could be that in the fanfiction, Kushina and Minato see Naruto becoming a great Hokage, respected far and wide. They might see him bringing peace to the village and forging strong alliances with other nations. This would make them extremely proud as they watch from whatever afterlife or special visionary state they are in.
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.
There could be a plot twist where they are revived in a different time period. Maybe they are brought back during the era of the Sage of Six Paths. This would mean they have to adapt to a very different world with different rules and powers. Another plot twist could be that when they are revived, they are linked to an ancient evil. They have to fight this internal connection while also trying to figure out what has happened to the ninja world in their absence. Additionally, it could be that their revival was actually a test by the gods of the ninja world to see if they can bring about a new era of peace.
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.
One common plot twist could be that Naruto sees a future where his friends turn against him, but then discovers it was an illusion created by a new enemy. Another might be that he sees a future where Konoha is destroyed and has to find a way to change that fate. Maybe he sees a future where he becomes a villain himself and has to struggle to prevent that from happening.
Perhaps there was a curse or a disease that he couldn't overcome. In some fanfictions, they like to introduce unique and deadly diseases that not even the best medical ninja can cure. It could also be due to a failed mission where he was caught in a trap that was impossible to escape from, leading to his death.
Perhaps a plot twist is that they are resurrected in the wrong era. They end up in a future where the ninja clans have all but disappeared and they have to find a way to bring back the ninja way. Or, they are resurrected with different powers than they had before. This change in power could lead to them being feared by the current ninja generation, and they have to prove that they are on the side of good.
In many Naruto fanfictions where Naruto meets Kushina and Minato, it often creates a very emotional scenario. Naruto finally gets to meet his parents who he has only heard about. It could be a heart - warming reunion where they share stories, hugs, and Minato and Kushina get to see how far Naruto has come.
On a more personal level, they could face internal guilt. As Naruto grows up and achieves great things on his own despite their neglect, Minato and Kushina may realize what they've missed out on. This realization could cause them a great deal of internal turmoil and regret for not being there for their son when he needed them.
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.