"why are you here?" is a simple question. You can tell because the verb "you are" has been inverted. You would hear it in direct speech. "why you are here" is a statement. However, you can also hear it in indirect speech. Examples: 'Why are you here?' she asked. My mum shouted at me, 'why are you here?' I heard a faint voice saying, 'why are you here?' The reason why you are here is to help us. Why you are here is not an easy question to answer. Who knows why you are here!

"This is the reason why you are here." The first would be used in a statement like this, for example. "Why are you here?" Used primarily in question form.

"why you are here" =is followed by the reason you are here. "Good morning, thank you all for coming let me tell you, why you are here" no ? is required "why are you here?" = is a question, in speaking there would be a stress on here, for writing you must have a ?

Here's my thought : "Why are you here" is a question that asks for the reason. "Why you are here" usually doesn't appear alone. This kind of structure is used to 1. explain the reason. 2. Be the second question in an Interrogative Sentence. For example, 1. "The party is the reason why you are here." 2. "Can you tell me why you are here?" Feel free to correct me if I am wrong.