In 2019, Chicago is placed under martial law after a global extraterrestrial invasion. As the Drummond family attempts to flee the city, they break through a barricade but are confronted by the aliens, who vaporize the parents but leave their sons Gabriel and Rafe alive.
By 2027, the world has capitulated to the alien “Legislators”, submitting to their governance. Humans are conscripted to build “Closed Zones”, underground habitats for the aliens with access only granted by high government officials.
Gabriel Drummond (Ashton Sanders), living in the impoverished Pilsen neighborhood, is confronted by Chicago Police Special Branch Commander William Mulligan (John Goodman), who was partnered with Gabriel’s father before the invasion. Mulligan is convinced that the Phoenix resistance group has not been neutralized, contrary to what the public has been told, but Gabriel offers him no information.
Gabriel meets with a member of Phoenix to sell a hand-rolled cigarette containing secret information received from a coworker. The man takes him to Wicker Park, where he meets his brother Rafe (Majors), the leader of the resistance. Rafe takes the coded cigarette and directs Gabriel to leave as Phoenix is planning to attack the upcoming Unity Rally at Soldier Field. Rushing to his apartment and hastily packing, Gabriel is again confronted by Mulligan, who had him under surveillance. Gabriel evades Mulligan and hides underground.
The cigarette’s code allows Rafe’s team to access Chicago’s surveillance system and the deployment patterns of law enforcement units. Rafe and other Phoenix members attack the Unity Rally, using an invisible alien explosive device against the aliens when they arrive. The attack initially appears successful, but the city is subsequently locked down and swarmed by security forces in response. Angered by the attack, the aliens bring in hunters from off-world to seek out the perpetrators, finding Rafe and his accomplices Anita (Caitlin Ewald) and Daniel (Ben Daniels). Anita is vaporized and Daniel ingests a cyanide pill to avoid capture, but Rafe is shot and arrested by Mulligan before he can take cyanide.
Gabriel emerges from hiding but is taken into custody during a police raid. Mulligan shows him his brother being tortured for information and convinces him to send a message through the Phoenix network in hopes of meeting the supposed ringleader, Number One. Gabriel is eventually led to Jane Doe, a prostitute running a brothel in Pilsen, who acknowledges him by name, confusing Gabriel. Police raid the house, and Doe is killed.
The subsequent investigation reveals that Doe bugged her own residence to record conversations with Special Branch members and glean classified information. The tapes reveal that Police Commissioner Eugene Igoe (Kevin Dunn) divulged sensitive information about the aliens’ arrival to Soldier Field which allowed Phoenix to develop their attack strategy. Igoe, along with Rafe and many others, are deported off-world and Mulligan, declaring the Chicago threat neutralized, is promoted to Acting Commissioner.
Mulligan meets with Gabriel privately, with Gabriel lamenting that Rafe’s plan failed. Mulligan, retrieving a box earlier received from Doe, reveals a BlackBerry phone, giving the memory card to Gabriel and suggesting that failure was the plan all along. Gabriel reviews the card’s contents — a video depicting his own baby shower, and revealing Jane Doe taught at the same school as his mother. It was at the shower that she was introduced to Mulligan, with several Phoenix members present, and the video closes with Mulligan leaving a message for Gabriel, inspiring him to carry the torch of Phoenix.
Meanwhile, Mulligan is cleared to meet with the Legislators underground. As he descends, the invisible substance of the powerful alien explosive envelops him, indicating he is part of the resistance and that the whole ‘failed’ plan was orchestrated to allow him to deal a fatal blow to the Legislators.
During the credits, a map details that the Closed Zone was successfully destroyed, with other resistance strikes and protests having broken out in cities all over the world, indicating that the opening exhortation to “spark a match and ignite a war” has led humanity to attempt to overthrow their alien oppressors.