In Tangier, the private security firm Byzantium pulls off a daring raid, in which the team fakes the death of one of their own operatives in the course of freeing a prisoner. Following the mission's success, the agent, Sam Hunter, makes plans to meet with her fellow operative and secret lover Aidan Marsh at Café Khalil at 4:00-she's going to tell him she's pregnant. When the time comes, it's not Aidan who arrives, but a wave of armed thugs, one of whom shoots Sam in the abdomen.
A year later, in a remote region of Scotland, Sam recovers from her injury, regroups and retrains. She keeps a wall of information with clues on both her target and her team, as she tries to figure out who betrayed her. When she's regained her full strength, Sam returns to London and purchases a small flat where she sets up a secret room for her wall of clues. Arriving unannounced at Byzantium, Sam surprises her boss Rupert Keel, team leader Alan Crane and fellow agents Hasan Mousa and Zoe Crane, as well as new operative Ian Fowkes. Aidan is most shocked of all. He tracks Sam back to her home, and she tells him how she escaped from her attackers, but she's reluctant to trust him. Once he leaves, she takes out his cellphone-which she lifted off him-and clones the device, revealing a voicemail from a mysterious female caller: "I'm here, you're late."
Sam gets back to work, and Byzantium launches a new mission. Their mysterious client plans to bid on the Upper Khyber in Pakistan. Before they do, they need an agent to gain access to their chief rival, the powerful and corrupt multi-millionaire Jack Turner. To do so, Byzantium stages a fake kidnapping of Turner's grandson Eddie. Sam, posing as an unemployed American teacher named Alex Kent, saves the boy from Hasan's "kidnapping" attempt. The boy's father, Stephen, takes a liking to Alex and invites her to live with them as Eddie's teacher.
Sam installs cameras in the Turner household. Meanwhile, there's another man who has been keeping tabs on her from afar. The Blank-Faced Man takes out a scientist named Horst Goebel and impersonates him to gain access to the Turner home.