There might be a shadowy organization that is the main antagonist. They could have blackmailed Grayfia into betraying Naruto. This organization would be pulling the strings in the background, using Grayfia as a tool to achieve their goals, which might include taking over the ninja world or something equally sinister. So, while Grayfia is the one doing the betraying, the real force behind it all is this organization.
It could be the one who manipulated Grayfia into betraying Naruto. Maybe it's a powerful and cunning villain from Naruto's world or even from another dimension. This antagonist could have a hidden agenda that involves getting rid of Naruto by using Grayfia.
Perhaps Grayfia herself becomes the main antagonist after the betrayal. Since she has turned against Naruto, she now poses a direct threat to him. Her actions and decisions would be centered around causing harm to Naruto and his allies. Even if she was initially tricked into the betrayal, her continued actions against Naruto would make her the main source of conflict.
Grayfia in this fanfiction might be a powerful figure. She could be a ninja with unique abilities or a non - ninja with influence in the Naruto world. Since she betrays Naruto, she probably has her own set of beliefs and goals that conflict with Naruto's. Maybe she's part of a secret organization or has a personal vendetta against Naruto that we'll find out as the story progresses.
In a 'grayfia betrayed naruto fanfic', perhaps Grayfia is tricked into believing Naruto is a threat to her world or someone she loves. So she decides to betray him. It might start with her subtly sabotaging Naruto's missions. As the story unfolds, Naruto discovers her betrayal and has to decide whether to forgive her or take revenge. And Grayfia may later realize her mistake but it's too late to easily fix things.
Well, it could be that Grayfia somehow misinterprets Naruto's actions and believes he's a threat, leading to her betraying him. Maybe she's been influenced by some outside force or false information.
The Konoha elders could be the main antagonists. They are often shown to be quite traditional and set in their ways in the original series. If Naruto goes against their old - fashioned ideas about the village's future and ninja code, they would likely oppose him strongly and could be the driving force behind making Naruto an outcast, which in turn could lead to his 'betrayal'.
If Rias betrays Naruto, she herself could potentially be the main antagonist. Since Naruto is usually seen as a protagonist, Rias' actions of betrayal would put her in direct opposition to him. Her motives and actions would then drive the conflict in the story.
Friendship or an unlikely bond can be a major theme. Since they are from different universes, the fanfic may explore how they form a connection that goes beyond their initial differences. It could be based on mutual respect for each other's abilities or a shared goal.
I'm not aware of any such fanfic, and this kind of description involves inappropriate and vulgar content. Fanfics should generally be based on positive, creative and appropriate themes.
It could be the very villagers who once looked up to Naruto. Their betrayal could turn them into antagonists as they might try to further harm Naruto to protect their own interests.
Danzo could also be the main antagonist. He is known for his underhanded methods and distrust of anyone with too much power. Since Naruto has the power of the Nine - Tails, Danzo might spread lies within Team 7 to make them think Naruto is a danger, causing them to betray him.
Definitely Naruto and Grayfia. Naruto is the main protagonist who has his own story and growth arc. Grayfia is the one who changes Naruto's life by adopting him. She could be a noble or a powerful mage. There may be other characters such as servants or comrades of Grayfia who are initially skeptical of Naruto but later come to accept him. And of course, there could be antagonists. Maybe there are some rivals in Grayfia's world who don't like the idea of an outsider like Naruto being in their midst and they try to cause trouble for him.