Mueller is not an independent prosecutor. He cannot indict anyone without first reporting this to the DOJ official who is responsible for overseeing him. If Sessions is no longer the AG and therefore his recusal is moot, then I don’t think the Deputy AG has any role to play anymore in overseeing Mueller.
DAG is responsible for all day to day operations. All reporting of the DOJ goes through the DAG, except maybe the OIG, which also reports directly to Congress.