During the events of the Civil War, S.H.I.E.L.D. was headed by Commander Maria Hill. The organization was tasked to oversee registration, and capture Anti-Reg heroes. When the their nanite control system gained sentience (revealing said "intelligence" in Prison 42), they were forced to call a truce with the White Star. Several months after the Fold's defeat, almost half of the already-registered heroes left (due to not being forced into mandatory police services), and Maria Hill being named the new director (she had been acting director on the U.S. President's orders after Nick Fury became wanted for questioning after the Latverian siege on New York).