During the "Civil War II" storyline, Elektra applied to join S.H.I.E.L.D. in order to free her conscience of the deaths of the passengers of the crashed Black Hawk. She took the position of field director when Phil Coulson left the group. When Coulson was trying to interfere with Captain Marvel's plans to use Ulysses Cain's abilities to stop crime before it happens, Elektra discovered that Leo Fitz was Coulson's mole in her group which Maria Hill was alerted to. At the same time, she also reinstated Grant Ward into S.H.I.E.L.D. and placed an explosive collar on his neck to ensure his loyalty.