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 ISIS's 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 hug 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.
The DGSE no longer knows whom to trust with its missions and its agents. Malotru and Sabrina are set to meet the French jihadist at the Syrian border.
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 ISIS connections, as a way to reach Boumaza in Syria.
The suicide bomber pulls out of the mission against Boumaza, and Debailly steps into the operation, travelling to Syria but swearing his team to secrecy. He finishes his letter to Prune. DGSE hears that Marina is being interrogated by the Iranian secret police, who are torturing Zamani. The DGSE meets the CIA and insists that they identify the mole; after being threatened, the Americans name Debailly. Prune finds Debailly gone from his flat, reads his letter, and alerts the DGSE.
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 hug 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.