“What are you doing here?”
You're at a hip-hop concert. You run into someone that you work with. You didn't think he liked this kind of music, so you're surprised to see him there. When you first see each other, you say this.
What are you doing here?
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What are you doing here?
This question means "Why are you here?" But "Why are you here?" sounds rude and accusatory (it sounds like you're accusing the person of doing something wrong). You ask "What are you doing here?" when you see someone that you didn't expect to see in that place.
This phrase is pronounced with stress on the word "you":
What are you doing here?
If you give this sentence the wrong intonation, it can sound rude as well. Use a high intonation for "you" and remember to smile!
What (is) (someone) doing (description)?
When you use "What are you doing" to mean "why", there are several different descriptions that you can add to the end of the phrase. You can add location words like "here" and "there":
What were they doing there?
Or phrases that describe the location and start with "in", "on", "at", "behind", and so on:
What's she doing at the meeting?
You can also describe what someone is doing at the time:
What are you doing talking on the phone? We need your help!