It is the start of a question asking what is inside something. What is in the box? works like that.
The noun after the decides what you mean. What is in the drawer? asks about the drawer, so context changes the question.
Watch the nearest mix-up: Who is in the room? asks about people, not things. Keep the order what is in the plus the thing.
The word the points to a specific thing both speakers already have in mind, like a fridge in your kitchen. Asking What is in the fridge? means you both know which fridge, and you want to know what it holds. Swapping what for who changes the question from things to people: Who is in the room? asks about a person, not the contents. It is the question word, not the rest of the phrase, that sets what the question is about.