When “What are you gonna do?” means, “That’s just how it is, so just accept it.”
Example sentence: “We have too many items for the express lane, so we have to get in line behind 10 people in the regular lane. (Shrug) Well, whattaya gonna do?”
In European Spanish there’s a fairly direct equivalent “Qué se le va a hacer.” -What can you do (about it)- or even “Qué le vamos a hacer.” - What are we going to do (about it).
I would imagine in this case, it’s closer to the meaning “nothing (else) can be done about (the situation).”
So a quick translation to Spanish could be, “No se puede evitar.” meaning “It can’t be avoided.”
“Ni modo” works. It’s a common expression meaning “oh, well,” and can convey “that didn’t work, but what the heck, life goes on.”