It could be that there is no traditional antagonist. The conflict might be internal, with Naruto's own emotions towards Kushina being the main source of drama.
However, if there has to be an external antagonist, it could be a dark force that tries to manipulate Naruto's confrontation with Kushina. Maybe a spirit that wants to use their emotional turmoil for its own evil purposes, like causing chaos in the ninja world by disrupting Naruto's connection with his mother.
In this fanfiction, perhaps Naruto confronts Kushina about the secrets she kept from him. For example, if there were things she knew about his powers or his destiny that she didn't share before her death. He could be feeling betrayed and wants answers.
It could be someone who took advantage of Kushina's leaving. Maybe a rogue ninja who wants to use Naruto's vulnerability to their advantage. They could try to turn Naruto against the village by making him believe that the village drove Kushina away.
Perhaps Kaguya Otsutsuki is resurrected again, but this time with a stronger will and more dangerous plans. Since Naruto was the one who played a major role in defeating her before, she targets him first in this fanfiction.
It could be an old enemy of Kushina's who was thought to be dead but has now returned. Maybe someone from her days in the Uzumaki clan who has a vendetta against her and now sees Naruto as an obstacle too.
It could be Orochimaru. He's always been interested in powerful ninja and their abilities. Since Kushina has strong chakra and a connection to Naruto, Orochimaru might see her as a valuable asset to either experiment on or use as bait for Naruto. He's devious enough to come up with a complex plan to capture her.
It could be Orochimaru. He might have manipulated Kushina into kidnapping Naruto. Orochimaru has always been interested in the power of the Uzumaki clan and Naruto's nine - tailed fox power. He could be using Kushina as a tool to get to Naruto.
Maybe a new, powerful and evil ninja from another land. This ninja could have come to the village and caused a lot of chaos, making Naruto believe that no one in his village was capable of protecting themselves or him. So he blames everyone for their weakness and starts to hate them all, with this new ninja being the root of the problem.
It could be a corrupt ninja from another village who wants to get rid of Naruto as he sees him as a threat to his own plans. This ninja could have framed Naruto to send him to prison.
Another possibility is that there is no single main antagonist. It could be a combination of misunderstandings, village politics, and personal issues within Kurenai herself that lead to her betraying Naruto. For instance, the village elders might be pressuring Kurenai to keep Naruto in check, and at the same time, Kurenai has her own doubts about Naruto's power which could be misconstrued as a reason to betray him.
It could be one of the harem members who has a hidden dark side. Maybe she's jealous of Naruto's closeness to others in the harem and decides to turn the rest against him, so she becomes the main antagonist.