Word Meaning – What Does ‘What Do We Have Here’ Mean?

It means, "what [situation/object] do we have here?" That is, it could mean either, "what is happening here?" or, "what is this?" It would typically be used to ask for an explanation on what has recently happened in this location or an explanation on what an object is.

It is not quite equivalent to, "what are you up to?" Although the questions can often be used interchangeably, this is not always so. You could ask others, "what are you up to?" when confronted with a strange situation, implying that it was they who were the cause of this situation. "What do we have here?" would not carry this implication.

An extended example of this distinction: a detective arriving at the scene of a crime might ask, "what do we have here?" of his team who have begun investigating. He would expect a response listing the facts that his team has discovered about the crime. Asking instead, "what are you up to?" would suggest that he wants to know about what the members of his team are currently working on. If the detective were to then notice a stranger leaving the crime scene, he might ask him, "what are you up to?" This would come across as accusational, but reasonable in the circumstances. Asking him instead, "what do we have here?" might suggest the detective expects the stranger to know some facts about the situation and could also imply that the detective is suspicious of the stranger. The detective could ask of his team, "what do we have here?" in reference to the stranger, perhaps hoping for them to identify this person or to draw attention to him. If the detective were to later be shown an object from the scene of the crime he might ask, "what do we have here?" to have the significance or the purpose of the object explained to him. Asking the individual showing him the object, "what are you up to?" would not elicit a helpful response - what he is doing is showing the detective an object. Finally, if the detective were to catch a criminal in the act of committing a crime, he may use the question, "what do we have here?" rhetorically to indicate that there is no reasonable explanation which the criminal could use to justify himself. This is perhaps one of the most common uses of the phrase. In this context, "what are you up to?" would essentially be equivalent, though perhaps would be more likely to receive a response.

This example was chosen for the reason that the question, "what do we have here?" is perhaps most commonly found in police procedural dramas and films, although it is not exclusive to them. It is uncommon to use it in conversation - the suggestions in the first paragraphs would more often be used instead.

It may be helpful to see https://english.stackexchange.com/questions/51604/origin-of-well-well-well-what-do-we-have-here.