What does Que esta haciendo mean?

¿Cuál de las dos opciones? Porque no me queda claro:

... que está haciendo --- ... who / that is doing...

¿Qué está haciendo? --- what are you doing (formal you singular); what's he / she doing?

Please! Write clear and correct contexts to avoid these terrible confusions.

it means: what is he/she/it doing? esta can also be used for the formal you (usted)