“What are you doing up at this hour?”
You wake up in the middle of the night because you hear some noises. You go to see what the noise is, and find your daughter awake in the kitchen and making a snack. You ask this because you want to know why she's awake now.
What are you doing up at this hour?
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The phrase "What are you doing ___?" means "Why are you ___?". It also expresses a feeling of surprise, and sometimes accusation:
What are you doing calling my house in the middle of the night like this?
You can see from the examples above that "What are you doing" can be followed by a word like "here". It can also be followed by "there", a prepositional phrase like "on the roof", and so on. Or, like in the example at top, it can be used with "___ing":
What the hell are you doing calling my wife?
"Up" can mean "awake":
Is Laney up yet?
A: I'm sorry, were you asleep?
B: No, I was up.
"At this hour" is a phrase that means "at this late time of night".