Thomas Egan (Ethan Hawke) is a former pilot that is forced into doing drone piloting as that has become the future of the War on Terror. Egan's feelings of emasculation and the lack of morality of his job only intensify when the CIA, under the direction of "Langley" (voice of Peter Coyote) force his team to do jobs that result in numerous civilian causalities under the assumption that these losses are worth the saved American lives.
Egan begins to become unhinged and spirals into alcoholism due to his job. His wife Molly (January Jones) tired with his attitude and his unwillingness to be a present father and husband leaves him and takes the kids to Reno. When Egan deliberately loses a secondary target because the truck carrying them had a mother and child, Egan loses a promotion and is demoted down to traditional surveillance.
Egan speaks with Vera Suarez (Zoe Kravitz), his co-pilot who also objected to the collateral damage who tells him that she resigned, unable to deal with the destruction they caused. Shortly after, Egan tries to right one wrong, and targets a man, who while not a confirmed combatant, had raped a woman twice under Egan's surveillance. Egan turns off the recording modules and fires a missile, killing the man and to his horror, almost killing the woman too. She survives though, to his relief.
Egan leaves the base despite his commanding officer Johns (Bruce Greenwood) telling him to stop, effectively resigning from the military. We last see him in his car, driving to Reno, in order to get his wife and kids back.