Marina begins to socialise with young Iranians, including Zamani, the son of a well-connected minister. She finds adapting to the internal politics a challenge. The Americans fail to rescue Nadia in an ambush in Lebanon. Debailly threatens to withdraw co-operation; the CIA retaliates by threatening to betray him, then asks him to make a better offer. Debailly offers to share a prospective DGSE source within Iran's nuclear industry. The DGSE discovers that one of the IS executioners, Boumaza, is a French national.

Debailly recalls when he first met Nadia, and continues to agonise about her fate. The CIA confirms its interest in Zamani, but Debailly and Marie-Jeanne fall out over Marina's mission; Debailly persuades Deflot to replace her with him as Marina's handler. Debailly tells Marina to get close to Zamani. The Iranian secret police take an interest in Zamani and Marina. The French Government authorises action against Boumaza; Cyclone cultivates the jihadist's family, and Sisteron poses as a supportive lawyer. Duflot continues to hunt for the mole inside the Bureau. Nadia is held prisoner in Syria.

The DGSE recruits the jihadist's sister, planning to trap and kill Boumaza. Meanwhile the Iranian secret police continues to investigate Marina, and DGSE discovers this from a source. Marina is recalled to Paris, but leaves on an expedition before receiving the message, and is arrested. In Syria, Judge Badran interrogates Nadia about her affair. Duflot suspects that Dr Balmes, who has resigned from the DGSE, may have been the CIA mole, but fails to find any evidence.

DGSE receives a report that Nadia has been executed in Syria, but the CIA has warned Debailly to anticipate false reports, and agrees to work with him in return for his Iranian source. Marina is interrogated by the Pasdaran, then released, and she returns to Paris. Duflot tells Marina not to contact Zamani, who is coming to Paris, but Debailly then tells her to contact him again. Sisteron and the sister arrange to meet Boumaza on the Syrian border, where the Turkish military intend his capture. However, the sister is communicating secretly with her brother. Meanwhile, after a mock execution, Nadia is given her 'freedom', but forced to work undercover for the Syrian government representing its rebels abroad.

Duflot discovers that Debailly disregarded his order to Marina not to contact Zamani, dismisses him for misconduct, and reinstates Marie-Jeanne as handler. But Duflot's boss decides Marina should continue cultivating Zamani. Debailly maintains contact with the CIA. Nadia, visiting France, refuses to see him. Meanwhile, Sisteron sets out with Boumaza's sister to meet the jihadist. Turkish special forces extract Sisteron, but they are ambushed by jihadists and Sisteron is captured. Too late, DGSE discovers the sister's communication with Boumaza.

Boumaza takes Sisteron into Syria. DGSE decides not to attack, to protect its local agents. He hears that Turkish forces have his sister, and exchanges Sisteron for her, after cutting off his foot. DGSE ask Debailly back unofficially to lead a team to hunt Boumaza; he plans assassination using a suicide bomber. Duflot notices, from the GPS history of Debailly's phone, the weekend when it was untraceable (when he was with the CIA). He plants a bug in Dr Balmes's office. Nadia, in Paris, is reluctant to continue her role, but Nadim forces her; she contacts the DGSE for help. Celine arranges for Nadia to meet Debailly. Meanwhile, Marina returns to Iran, tasked with recruiting Zamani. Debailly passes her reports onto the CIA.

Continuing her meeting with Debailly, Nadia insists that DGSE help her escape from her forced role as figurehead for the Syrian rebels. Debailly decides to compromise Nadim by forging his application for asylum; he defects, and Nadia is taken away to a safe house. Debailly and Dr Balmes discover the bug in her office. The CIA stands Dr Balmes down from its service. Meanwhile, the French are close to securing Zamani as a source, only to find he has just been recruited by the CIA. Debailly continues to plan to execute the jihadist.

Dulfot goes to interview Marina personally about how the CIA managed to recruit Zamani. Marie-Jeanne wants to exfiltrate Marina, but she is overruled. Zamani gets caught texting his handler from an Iranian government meeting; his arrest leads to Marina's. Meanwhile, Duflot questions Nadim about Lefevbre, but he sticks to the answers Debailly had briefed him to give. Marie-Jeanne questions Nadia. Debailly writes a farewell letter to his daughter. The DGSE identifies a German journalist with IS connections, as a way to reach Boumaza in Syria.

Duflot lectures his team about loyalty, then offers to resign, but his boss refuses to accept. The DGSE investigates Debailly's disloyalty and interviews his colleagues. Debailly takes the suicide bomber's place as cameraman for the interview with Boumaza. In Iran, the CIA has agreed to trade one of its prisoners for Marina, but the Pasdaran try to kill her after encouraging her escape. However, she evades capture and is exfiltrated to France. In Raqqa, Debailly meets and kills the jihadist, but is himself captured and made hostage. Nadia opens the letter he left her, which expresses the same feelings about their love affair that she did, in the first episode of season one.