The city of Los Angeles has been occupied by an unknown force. Former FBI agent Will Bowman and his wife Katie are separated from their son during the invasion, and are willing to do anything to be reunited with him. When they are offered a chance to get their son back by collaborating with the occupational government, Will and Katie find themselves faced with the toughest decision of their lives.

Will faces unforeseen challenges on his first day at his new job. Katie receives her first assignment. Maddie reconnects with an old acquaintance. Carlos pays the price for Will's collaboration.

Katie's first mission forces her to question her commitment to the cause. Will's search for Geronimo doesn't sit well with the resistance. Bram's girlfriend shares a secret with him.

The second season opener has Will and Katie trying to keep their family together in the changing city. Broussard returns home while Snyder receives a job offer from a mysterious organization.

Will decides to trust an old friend. Jennifer visits Katie while Bram meets the camp commandant.

Will, Devon, and Charlie try to journey home. Katie, who fears the worst, says goodbye to her daughter. Bram makes friends at camp; and Maddie finds a new project.

Jennifer keeps an eye on the Bowman house. The family encounters unexpected challenges when Charlie returns home.

Will and Katie must save a fugitive from the occupation; at the camp, Snyder hides evidence; Broussard's cell is threatened by one of their own.

In the second season finale, the Bowman family must make an impossible choice following a revelation about the fate of the colony.