"We can not do what we want."
Translation:Kami tidak bisa melakukan apa yang kami mau.
I just spoke to an Indonesian friend I have and he said that in this context, apa is optional. It only marks a passive sentence. It's not something you really think about when you speak.
Dia suka apa? (What does she like?)
Dia suka buku bahasa Indonesia
Apa yang dia suka?
Yang dia suka (adalah) buku bahasa Indonesia
Both question mean "What does he/she like?" but in the 1st one the highlight is on dia, while in the 2nd one the highlight is on apa. So basically apa highlights/emphasizes WHAT (the thing) we actually want.