What do you think she's doing right now?

Literal

She [topic-は] now what [object-を] is-doing [quotative-と] think [question-か]?

Wh-questions embedded in 思う obey a quirk of Japanese syntax: the wh-word 何 doesn't move to the front, but the question particle か goes on the outer matrix clause, not the inner one. So 思いますか asks the listener directly — 'do you think?' — while 何 sits inside the embedded thought. English flips the wh-word forward; Japanese leaves it in place. The quotative と packages the embedded clause as the content of thought.