Perhaps it's a scenario where there's a prank being played. Some students have set up a magical practical joke that involves something flying around the classroom, and the protagonist tells Miss Granger to get under the desk to avoid getting hit by it. It could also be a lead - up to a more complex plot where Miss Granger discovers who's behind the prank and has to deal with them in a clever way.
Well, it could be a story where there's some sort of danger in the classroom, like a sudden spell gone wrong, and Miss Granger is told to get under the desk for protection. Maybe the teacher has a premonition and wants to keep her safe from the chaos that's about to ensue.
Another possibility is that it's a story set during a time of unrest in the wizarding world. There could be dark forces lurking around the school, and getting under the desk is a temporary hiding place. This could be part of a larger story arc where Miss Granger has to use her intelligence and magic skills to fend off the threats and protect the school and her fellow students.