DGSE tracks Debailly's attempts to contact Nadia. Dr Balmes meets her, and explains how Debailly got her released from captivity. Debailly sets up a plan to meet Nadia in a hotel, contacting her via her assistant's mobile, which DGSE is already monitoring for another operation. Meanwhile, Simon tells DGSE about Marina's call for help; he suspects she is being held in the hotel, and plants a microphone in her room. The agent is told that a Mossad team is coming to deal with her, which DGSE overhears. Marina is saved at the last minute when DGSE blow her cover. In Syria, the French pull out of helping the Kurds, but leave Esrin in place; she is killed in the fighting. In France, DGSE arrive at the hotel to apprehend Debailly, but Nadia warns him using their agreed code. Nadia is taken away, and Debailly disappears into the night.

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.

Mikhaïl Karlov receives a parcel with the USB key which Sylvain uses at work. Both surprised and worried, he tries to reach the young hacker and learns that the young man is on a mission in Seoul. Meanwhile, Alexis Bakatine, the head of security at the FSB, is continuing his investigation into the spy "Black September" in order to find out if Pavel is a double agent.

In Ukraine, Malotru arrives at the exchange location to get Marina. But on the way back, their convoy deviates from the route initially agreed upon by the DGSE, forcing him to warn Sisteron. Back in Paris, Marie-Jeanne quickly understands that Malotru’s life is at stake and confronts JJA and Ponte. Meanwhile, Jonas interrogates Iode 3 to try and prevent an impending terrorist attack in France.

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.

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.

DGSE mourns the loss of Duflot. Meanwhile, Mossad gives Marina the memory stick with the virus, which DGSE manages to copy before Marina successfully introduces it into the system. In Iraq, Cochise and his IS fighters take Debailly toward an arranged ambush with French special forces. Before they arrive, one of them becomes suspicious and stops the convoy; the CIA makes a drone strike on the support vehicle. Cochise is wounded in the fighting; the French forces arrive in time to rescue Debailly, who is put on a ship to Libya. The CIA insist on debriefing Debailly first; DGSE reluctantly agrees on condition that Dr Balmes does the interview. Later, Debailly escapes from the ship.

Sisteron warns Marina that her cover has been blown, but that her arrest could help on another crucial assignment. Meanwhile, Malotru parts ways with Samara and comes back to France, where he is to be held in solitary confinement. Back in Syria, Jonas has lost Iode 3’s track and must turn to artificial intelligence to try and find him.

Shahanah is murdered by the Iranians. DGSE sets up a secret meeting between Duflot and Cochise near Jarabulus, and Duflot prepares for his mission. Lely asks to meet Nadia again, and DGSE suspects IS may have lost Debailly; their agents in Iraq confirm he has escaped. Meanwhile IS catch and kill the Russian spy, but Debailly manages to evade capture.

Cochise refuses to spy for DGSE within IS, wanting exfiltration. Duflot agrees, if Cochise can free Debailly. Before he can return, Duflot is shot by one of Cochise's men; he is taken to hospital but later dies. Cochise obtains custody of Debailly. Meanwhile DGSE identify that Mossad plans to use Marina to infect the Iranian nuclear programme with a computer virus, which will subsequently allow them to disrupt it, via the seismic monitoring system linked to Baku. Marina panics again when she discovers the Iranian connections of her new security manager, and tries to flee but is intercepted and reassured by the Mossad agent.

DGSE discovers that Debailly is using the stolen IDs of former agents to travel back to France. Nadia hears from her assistant's Iranian contact that Debailly is free, but DGSE refuses to tell her anything; they use Prune to tempt Debailly into making contact with her. Debailly uses burner phones to contact Prune, and then gets a message to Nadia. Meanwhile, the Mossad agent tells Marina that her mission is completed. Before he leaves he realises that Marina has not been telling him the whole truth about herself, and begins to suspect that she is a spy. He confronts her and holds her captive. Marina uses their agreed code to call for Simon's help.

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.

Debailly asks DGSE to help Nadia, but is refused. He attracts the CIA by approaching the Syrians, purporting to represent the Americans, and takes time off to meet the CIA (revealed as the flashforwards shown from Episode Two). Dr Balmes suggests his motivation is not love for Nadia, but craving for the double life he experienced undercover. He agrees to return to the DGSE as a CIA double agent. Meanwhile, Marina disappears in Tbilisi en route to Iran, kidnapped by the Georgian secret service to see from where she seeks help. Cyclone is rescued in an ambush near the border with Mali.

Debailly manages to escape into the hills, and seeks help from a farmer who betrays him to IS, and he is recaptured. French agents identify the area where he escaped, but arrive too late. In Baku Marina gives her presentation to the conference, and is offered a job there, which Mossad urges her to take; she agrees after consulting DGSE. She panics when asked to take a polygraph, but is trained by Mossad on how to pass. In Syria, Esrin takes Duflot to his clandestine meeting with Cochise; however, Cochise is followed across the river by two of his men.

Chased by the DGSE and the CIA all the way to Moscow, Malotru tries to negotiate his return to France. The DGSE’s new head of Internal Security, JJA, initiates a full-spectrum audit of The Bureau and its new chief Marie-Jeanne, with the clear-cut intention of severing a few heads in the process.

Dumped by the DGSE, Malotru comes out of hiding and is quickly located by the Russian secret services. At the DGSE, Liz manipulates Sisteron to cause distrust between he and Marie-Jeanne. Meanwhile, Jonas begins to suspect that his mission might be hiding an ulterior motive: to ultimately eliminate the Jihadists he has been targeting.

Arrested for Espionage by the Russian secret services, Malotru is tossed aside and left to the mercy of other inmates. Back in France, the DGSE is striving to understand his motives before making a move. Marina’s phone has been hacked and used in a cyberattack against the Boulgakov Centre. Back in Iraq, Jonas suspects that a seemingly repentant Jihadist may be playing him to sneak his way back to France.

JJA is told to go ahead and recruit Mikhail. He contacts Pavel in Moscow to develop a strategy. Sylvain is sent to Seoul by the Russians to enlist Yellow Joon, a genius hacker. In Paris, Sisteron admits having lost confidence in JJA. In Cairo, intelligence indicates an attack is imminent.

Debailly continues to investigate the leads on Cyclone. Nadim traces Debailly's daughter Prune and starts asking about him. Marina and another agent force a colleague at the Institute to refuse the secondment to Iran. Debailly realises that the Syrians and Russians are tailing him, and finally tells Duflot about Nadia and her involvement with the Syria talks. Meanwhile, the DGSE identifies who is holding Cyclone for ransom in Algeria.

Nadia refuses to betray her country, and is angry at Lefevbre's revelations. Ill from the stress of her situation, she confesses to Nadim, and is flown back to Syria. The Russian FSB confronts DGSE and buys its silence. In Algeria, DGSE fails to plant a bug on the General holding Cyclone; Cyclone is handed over to ISIS. Marina is trained to deal with interrogation by Marie-Jeanne, tested by an Iranian agent pretending to be Reza's wife, and offered the Iran secondment. In flashforward, Debailly continues to talk to the CIA; the Americans do not fully believe his story.

ISIS threatens to execute Cyclone; Debailly is asked to work on his rescue. Nadim tries to blackmail him with Nadia's life, wanting him to betray Syrian sources; Debailly refuses to do so. The Americans pull out of the Sahara operation; DGSE suspects they may have a mole. Marina is further tested before leaving for Iran. Debailly shares details of the rescue plan for Cyclone with his colleagues.

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.

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.