>>371
Forgoing context, yes, "なにを しますか?" can mean "What will you do?" or "What do you do?"
The を particle does mark the direct object of a sentence but doesn't take on any special meaning at the end of 何(なに). It may be strange for a native English speaker to parse the sentence "What will you do?" for a direct object, but just think of the を particle as designating the subject of an action. A way to make this clearer would to rephrase the sentence in S-V-O (Subject-verb-object) format, the one most common to English. It would then become "You will do what?", where "You" is the subject, "will do" or simply "do" is the verb and "what" is the (direct) object. "何を～" is a common construction in Japanese.
-あなたは---何を作ります---か？
-What will you make?
-彼はお前のお兄さんを殺したばかりだ、---何をする---つもりですか？
-He just killed your brother, what do you plan to do?
You both correct and incorrect to translate "なにをする" to "what do?". Correct in that it "literally" means that but incorrect in that, once translated to English, it obviously doesn't make grammatical sense. Translating Japanese to English or vice-versa is more about finding the 'closest' meaning and not necessarily a verbatim translation. "What do?" will then become "What do you do?" or "What will you do?".
To establish just who is doing this doing, you need context. That may seem obvious but in Japanese the subject of a sentence isn't often required and must be implicated with context. Meaning she, he, it, or you could all be the subject of "なにをします？" but it is most certainly "you".
The sentence "what are you doing?" is slightly different and would be "なにをしているか？/なにをしていますか？", literally "what are/is (you/he/she/it) doing?