In some cases, the antagonist could be a group of magical creatures that have been wronged by wizards in the past. They see Hermione as a representative of the wizarding world and when she is left behind, they try to make her pay for the past wrongs. These creatures could have unique powers and abilities that make them a formidable foe for Hermione.
It could be a powerful ninja from another village who sees Naruto's godlike powers as a threat to his own plans of domination. Since Naruto is already feeling vulnerable due to his family leaving him, this antagonist might try to take advantage of his emotional state.
It could be a new dark wizard who rises to power in the wizarding world. This wizard blames Harry for leaving and believes that his departure has made the wizarding world weaker. So the new dark wizard sends his minions to the Muggle world to force Harry to return to the wizarding world and face him, or else he will start causing chaos among Muggles which Harry has come to care about.
It could be a jealous fellow trainee. This person might spread false rumors about Naruto, which leads to him being left behind in training. The jealous trainee doesn't want Naruto to get stronger and be more popular.
Another possibility is a dark wizard or a group of dark wizards who are after some powerful magic that the Lestrange family has, and Hermione gets in their way as she tries to protect the family or uncover the secrets. They would be the main force that Hermione has to face and overcome throughout the fanfiction.
Perhaps a powerful magical being from a different realm is the antagonist. This being might mistake Hermione for someone else or see her as a key to something in the wizarding world. So, it uses its magic to make her disappear. This being would be very difficult to defeat or negotiate with, making it a huge challenge for those trying to find Hermione.
It could be a jealous wizard who wants to steal Fudge's lemon - related magic for his own glory. This wizard might try to frame Hermione for stealing it first so that he can get her out of the way.
One potential main antagonist could be a disgruntled professor. This professor might feel that Hermione is too much of a know - it - all and decides to deage her as a form of punishment. Or it could be a Death Eater who has infiltrated Hogwarts. They know that Hermione is a valuable asset to Dumbledore's side, so they deage her to weaken the opposition. The Death Eater could then use the deaged Hermione as a pawn in their evil plans.
It could be a jealous figure skater who sees Hermione getting too close to their idol or a rival skater. This person might try to sabotage Hermione's attempts to be involved in the figure skating world, like spreading false rumors about her or causing problems at the skating rink.
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.
It could be a power - hungry student who wants to undermine Hermione and Favo Prefect. This student might be jealous of their status as prefects and the respect they get from teachers and students alike. So, they try to create problems for them, like spreading false rumors or sabotaging their projects.