The year is 2030 and six years have passed since the end of World War IV. Influxes of refugees are allowed into Japan to fill the labor gaps of the growing economy. Terrorist cells identifying themselves as the Individual Eleven have begun a series of ultranationalist attacks targeting refugee camps, foreign consulates and even the Prime Minister. A charismatic new leader rises amongst the refugee's resistance movement, a former memeber of the Individual Eleven. Simultaneously a top member of the Cabinet Intelligence Agency contacts Section 9 with shocking revelations and unknown ambitions regarding the current state of affairs.

When mysterious spacecrafts touch down across the globe, an elite team - led by expert codebreaker Louise Banks (Amy Adams) - is brought together to investigate. As mankind teeters on the verge of global war, Banks and the team race against time for answers - and to find them, she will take a chance that could threaten her life, and quite possibly humanity.