One reason could be a change of heart. Maybe Nagini realizes that Voldemort's cause is wrong and sees something in Harry that makes her want to protect him, like his kindness or his will to fight for good.
One reason could be a sense of kinship. Bellatrix might see a part of herself in Hermione's fierce loyalty and determination. Another could be a change of heart. Maybe she realizes the error of her ways and decides to protect Hermione as a way to atone for her past actions.
One reason could be to protect a family member's reputation. For example, if a family member made a mistake at work and it could lead to public shame, another might take the blame to shield them from that. Another reason is to maintain family harmony. If a younger family member is at fault and taking the blame from the parents would prevent a big argument or family rift, an older one might do it.
Another possibility is that he is in love with her. In fanfiction, love can be a powerful motivator. He might be attracted to her intelligence, her strong will, and her beauty. This love could override his loyalty to the Dark Lord and make him want to protect her at all costs. He could see her as a symbol of hope and a better future for the wizarding world.
Love. Maybe the Death Eater has fallen in love with Hermione secretly. It could be her intelligence, her bravery, or her kindness that attracts him. And this love overcomes his loyalty to the Death Eaters and the dark side.
One common reason could be his love for Lily. Since Harry is Lily's son, Snape might feel an obligation to protect him out of his undying love for her. It's like he's trying to preserve a part of Lily that still exists in the world through Harry.
Perhaps Voldemort discovers that there is a greater threat out there. In the fanfic, it could be that another dark force is emerging, and Voldemort sees Harry as an ally of sorts against this new threat. So, he decides to protect Harry in order to deal with this common enemy.
One possible reason could be that Naruto feels betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him question whether it's worth protecting. For example, if he finds out that the village elders were involved in unethical experiments or unjust actions against certain groups. Another reason might be that Naruto has different ideals now. He could believe that there are more important things in the world than just protecting Konoha, like bringing true peace to all nations without focusing on one village's interests.
One possible reason could be that he sees something in Hermione that reminds him of someone he once cared about. Maybe her intelligence and courage make him respect her in a way that he didn't expect, and this newfound respect leads to his decision to protect her.