NE (呢) does not only appear in questions. When it does appear in questions, it usually follows an elliptical sentence with the part that is understood being omitted. Therefore, it is only used in context.
1. Asking the same question without repeating it
Where do you work?
In the Bank of China. How about you?
2. Asking a question in context
The predicate can be omitted from a question if it is understood.
Half of eight is four; what about half of six?
3. Asking about “whereabouts”
When one does not see who or what one is expecting to see, 呢 is used to ask “what happened to..?” or “where did…go?”
You came to see the movie by yourself? Where is your boyfriend?
It should be noted that sometime this question is translated as “where is?” However, it is different from “….在哪裡？” which is a question about the “location” of something or someone, not their “whereabouts.”
To ask the physical location of someone or something, use “在哪裡？”
Where is the post office?
Reference: YUFA! A Practical Guide to Mandarin Chinese Grammar