Gray Days by Hailey Edwards

The Black Hat compound is rubble on the ocean floor, the director hasn’t been seen since the explosion that demolished his life’s work, and old enemies have decided it’s open season on the remaining agents. Oh. And Arden has decided now is a great time for a surprise visit to force a confrontation with Rue.
Between holding the Bureau together, searching for her grandfather, and babysitting Arden, Rue has her work cut out for her. But her distraction allows her to be blindsided by a loss that fractures her very soul. Betrayal is a familiar sting for Rue, she barely feels it anymore, but this time? She might not survive it.