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.

While under intense pressure from the FSB to cooperate, Malotru is considering how to approach a cyber operations officer. Back in France, Marie-Jeanne seeks Mag’s advice, only to find out that JJA had coerced him to resign and that she could very well be next. Jonas hires an expert to infiltrate an Islamist financial network.

Just as Karlov is beginning to lose patience, Malotru suggests recruiting Ellenstein. Back at the DGSE, Marie-Jeanne is monitoring a cyberattack, hoping to track down the person responsible for hacking Marina’s phone. Meanwhile in Mosul, Jonas and Jean-Paul are searching for a way through the ravaged city to get to the Collector.

Under Karlov’s watchful gaze, Malotru initiates Ellenstein’s recruitment. At the DGSE, Sisteron suspects that Cesar is not ready to go on a mission and will not be able to hold his legend undercover. Back in Raqqa, still under Daesh’s occupation, Jonas and Jean-Paul join a battalion of Yazidi women to track down Iode 3.

In Moscow, Malotru welcomes César, who has taken Ellenstein’s identity. Back in Damascus, the Syrian authorities refuse to let either Jonas or Jean-Paul access the morgue, where Iode 3’s body most likely lies.

Karlov asks Malotru to join the FSB in Moscow. In Paris, Sisteron and the entire Bureau must answer to an inquiry questionnaire on Marie-Jeanne, which JJA intends to use against her during the next board meeting. Meanwhile, Marina is resenting the way the Bureau is using Micha, afraid to once again leave a trail of destruction in her wake.

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.

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.

Debailly is prisoner of IS in Iraq. DGSE asks Nadia to negotiate his release through an intermediary Shahanah, a corrupt art dealer, and promises her an EU Deputy Commissioner position in return for her help. Sisteron is sent to Iraq to meet Kurdish fighters and rescue him, but their attempt to do so during a sandstorm fails. He finds an SNCF railway points diagram left behind by IS, which DGSE believes is an attempt by 'Cochise', someone senior within IS, to communicate with them. Meanwhile Marina is working as a seismologist and is still traumatised by her experiences in Iran.

One of Debailly's jailers is a Russian FSB mole and offers to help him. Meanwhile, Duflot tries to help Marina overcome her trauma. Shahanah takes Nadia to meet Lely, a female intermediary for IS. Sisteron and Kurdish fighter Esrin are ambushed by snipers and she is injured, and flown to France for treatment. Sisteron suggests to Duflot that Esrin should be recruited in exchange for help with her son's education. Marina, plagued by panic attacks, resigns from the DGSE. The FSB mole is seriously injured in combat.

Debailly loses hope after his FSB helper is wounded, and stops eating. Marina is approached by Phillipe, a Mossad agent who is posing as DGSE and wanting to recruit her. DGSE advises her to accept the offer, and report everything back to them. Shahanah requires Nadia to launder stolen artefacts from Syria in return for his help with the negotiations, but she refuses to compromise herself. The FSB mole recovers in hospital, and returns just as Debailly is being filmed for a new hostage video by IS.

The CIA wants to bomb the camp where Debailly might be held, but DGSE insists they wait. Duflot wants to get Debailly released before he retires, but MAG reminds him that the agency doesn't normally make much effort to rescue disloyal agents. DGSE use Prune to pressure Nadia into agreeing to resume negotiations; Nadia meets Lely again and is given the hostage video. DGSE see that the points diagram has been altered to communicate that Cochise wants to defect. Duflot volunteers to go into the field and handle both cases himself. In Iraq, the FSB spy escapes into the desert with Debailly, with IS in pursuit. Meanwhile, Mossad persuades Marina to speak at a seismology conference in Baku. Simon, Marina's ex who works for DGSI, offers his help if she runs into trouble.

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.

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.

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 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.

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.

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.

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.

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 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.

Agent Malotru (Debailly) is recalled to Paris after six years undercover in Damascus, and ends his affair with Nadia El Mansour. In Algiers, agent Cyclone is arrested, drunk, despite being avowedly teetotal. Debailly struggles to forget Nadia and to return to a more normal working life. He is assigned to train Marina Loiseau, who will work undercover in Iran. Debailly discovers that Nadia is in Paris and resumes contact with her. Meanwhile, agent Cyclone has gone missing in Algeria.

Debailly is still under routine surveillance, whilst resuming his affair with Nadia under his cover identity Paul Lefevbre. He starts to question Nadia's reason for being in Paris. Meanwhile, the DGSE hires psychologist Dr Balmes, and asks her to review his state of mind. Agent Gherbi is exfiltrated from Algiers after hearing about Cyclone, and Marina continues preparing for her mission. The episode closes with a brief scene of Debailly recounting his story while connected to a polygraph.

Marina starts work at the Institute of Earth Physics. A brief scene shows Debailly, connected to a polygraph, continuing to recount his story. The DGSE interrogates Gherbi to confirm he is not also working for Algerian intelligence. Duflot's brother-in-law works undercover in the Sahara Desert. Meanwhile, Nadia's visits to Lefevbre arouse the suspicion of Syrian agent Nadim. Debailly digs into Nadia's background, and confronts her as to why she is really in Paris.

The episode starts with a flashforward of Debailly continuing to explain his story. Nadim investigates Paul Lefevbre, and tells Nadia not to see him again. But he finds them having dinner, and interrogates Lefevbre. Nadia confesses her true reason for being in Paris, and Debailly realises that their relationship puts her in danger. Meanwhile, Reza starts to flirt with Marina, and she has to rebuff his advances. DGSE tries to find out if the Algerians are holding Cyclone, and must stop his mother travelling there to search for him.

DGSE makes contact with Algerians holding Cyclone, and Sisteron goes to Algeria. The Syrians continue to investigate Paul Lefevbre, testing him by mugging him in the street. They also seek help from the Russians. Meanwhile, DGSE puts Marina through a surprise mock interrogation. DGSE is also concerned that Cyclone's capture could have compromised the Sahara Desert operation, in which the Americans are involved. In flashforward, Debailly continues to recount his story to the Americans.

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.

Debailly continues to be tailed by the Russians. The DGSE meet an Algerian with information about Cyclone. They decide to recruit Nadia; Marie-Jeanne realises that Debailly has not told her the full truth, and confronts him. She also helps Marina compel a second colleague to refuse the Iran secondment, and teaches Marina a lesson about not getting close to her contacts. Debailly continues to be interrogated by the CIA in flashforward; it is revealed that Dr Balmes works for the Americans.

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.

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.