Pregnant Sam Hunter is part of a team from Byzantium, a private security company completing the rescue of a doctor imprisoned in Tangiers when later in the day, alone, she is ambushed and badly wounded. A year later after recovering in Scotland she returns to her company in London, who thought she was dead, to take up her old job determined to find who betrayed her. Her boss, who is initially reluctant to re-employ her, uses her to infiltrate the home of a criminal turned multi-millionaire, Jack Turner, by befriending his widowed son through his child. A third party also arrives at the house having killed and now impersonating Dutch engineer Doctor Goebel.

Team member, Hasan, is kidnapped by Jack Turner, and Sam is ordered to kill him to keep him from being tortured and compromising the team. The bogus Doctor Goebel arrives to conduct business with Turner. Later that evening Sam takes the opportunity to kill Hasan but he reveals he has information on who tried to murder her in Tangier. Yet another man searching for Sam seeks out an old army colleague seeking her whereabouts and is murdered by the man. Later Sam meets the same man intending to kill her, Sam turns the tables, but he escapes. Realising he is linked with Hasan she returns to the cell to free him but he tries to kill her and she kills him inadvertently carrying out her orders.

Byzantium are manipulating the bidding to ensure their client wins the Upper Khyber Dam contract which requires Sam to continue undercover with the Turners. At the hotel where the bidding is being conducted Sam comes face-to-face with Bernard Faroux the Frenchman she seduced and betrayed in Tangier. He offers to tell her who tried to assassinate her but only if she finds out Turner's bid instead of telling Byzantium. Aidan is the mole working for MI6 liaison officer Natalie Thorpe but still remains undiscovered. Faroux's dying words to Sam reveal another mysterious organisation, "Hourglass". Turner wins the bid by overbidding £30 million he does not have.

Kismet is a software programme that Jack Turner uses to make his money with hedge-fund manager Lewis Conroy. Sam sets out to find the connection between the two men. Aidan discovers Sam's secret room and a note questioning what is Hourglass and calling in a favour with a secretary at Byzantium she finds out for him that Hourglass is a file held by George Ballard for the last 40 years and he is now MI6 head of section. Byzantium discover Turner has been profiteering from arranged accidents and needing £30 million another is planned. Fowkes discovers the location of the next accident and Aidan is sent to stop it while Sam is sent back to the Turners but in the street she is overpowered and sedated by the bogus Doctor Goebel.

Sam wakes in hospital and is visited by the bogus Doctor Goebel who tells Sam that he is trying to protect her from 'Hourglass'. Aiden exposed as the mole escapes from Byzantium and meets Sam. A meeting is arranged for Sam to meet Ballard at the National Portrait Gallery at a cryptic painting called 'Ambassadors'. Ballard reveals Hourglass is a conspiracy orchestrated by five multinational corporations and three of the seven members of the Byzantium board are CEOs of Hourglass corporations. Ballard is killed on leaving the gallery. Sam's investigation of the conspirators takes her and Aidan to a country estate where she had been years before where she was taken as a child after her mother was murdered and she was kidnapped. Byzantium, to protect Sam's cover, set up two innocent people and Jack Turner orders three more murders.

Sam sleeps with Stephen Turner to maintain her cover. Polyhedrus is the company that built the Khyber dam and one of the employees is the doctor she rescued in Tangier. Through an intercepted fax Byzantium suspects that Jack Turner intends to assassinate Fatima Zahir, a Pakistani presidential candidate opposed to the sale of the dam he is trying to buy and she has a secret meeting with the doctor. Fowkes is part of the assassination plot not realising he is the fall guy until it is to late. Stephen Turner realises how ruthless his father is and seeking information from a corrupt policeman receives a file revealing Sam's true identity. Keel is suffering from a terminal brain tumour.