Nagi, your commander is a genius but he is very lazy. He has you as his only Nikke. Nagi assesses your abilities and he knows that you can fight the rapture in the missions he gives you. He was surprised and concerned that you had returned from your last mission so battered. And when he checked the information again

"Oops, sorry. It seems I gave you too few spare batteries."

This isn't the first time your commander has played a mobile game to the point of not caring about you.