Following the attack which has left their headquarters in ruins, the Fly team race to apprehend Olivia Thornton who's escaped from custody and bring down Yusif Sydin for good with assistance from analyst Amanda Tate and as they struggle to come to terms with what's happened. The team try to get to Thornton by questioning her partner and son, but later release them due to lack of progress. However, as they later try to corner them in reuniting with Olivia, a hitman sent by Sydin kills her. The hitman is apprehended following a pursuit and cooperates and implicates Sydin in weapons dealing. Raines is hospitalized, suffering a serious injury to his leg, which he could risk getting amputated. However, Assistant Special in Charge Jubal Valentine of the New York field office manages to call a doctor over to work with Hungarian doctors to save his leg. Jamie decides to return to the US, relocating to the Washington DC field office.

• This episode marks the final appearance of Heida Reed (Jamie Kellett). It also marks the debut appearance of Christina Wolfe (Amanda Tate) while Jeremy Sisto (Jubal Valentine) is credited as a Special Guest Star.

Nine years ago, FBI agent Bill Cormack and four other contractors were abducted and assumed to have been killed in Tripoli, Libya. In present day, Cormack's daughter Beatrice receives a call that indicates he is alive. Forrester and Powell are dispatched undercover to the notorious Qamar prison outside of Tripoli in an attempt to break Cormack out and bring him home. However, along the way, both they and Smitty find their guard informant turning on them and must improvise Cormack's extradition. With the reluctant help of fellow inmate Hassan Abdallah, they manage to get Cormack out and back to safety and reunited with his daughter. Additionally, two of the other contractors are also rescued while also revealing that their colleagues died during the interrogation they were subjected to after they were captured. Raines makes a gradual recovery and is cleared for desk duty. The team settle in to a refurbished and upgraded HQ, while Vo is promoted to second-in-command.

• This is the first episode where Jeremy Sisto (Jubal Valentine) isn't credited as a Special Guest Star. Instead, he appears under the list of Guest Stars for the episode, receiving the "And" credit.

The sweet sixteen celebration of Emily Lambert is cut short when her mother Diane is found shot and killed at the family estate in Monaco. The Fly Team travel there to assist the Monegasque police with the investigation. When satellite recordings from the property are ceased by the brother-in-law, they learn that he had a motive to seize the family fortune following Diane's death, but is backed by an alibi. Further deciphering of the recordings lead them to an old flame of Diane from Omaha, Nebraska, Connor Boyd, who has arrived in Monaco seeking to retrieve his share of the fortune after killing Diane. He takes Emily hostage at a local coffee shop and demands a clear path for them both to exit. Vo enters trying to negotiate, and Boyd is tackled following a disruption through a TV with a recording of Diane. Powell begins to distance himself from Vo, explaining that he thinks she has more chemistry with Raines than him.

Mark Shaw, a notorious criminal and womaniser, is tracked down to Sofia, Bulgaria, where he is exploiting underaged girls. The team head over to apprehend him on previous charges, but are halted by Bulgarian police, who cite incorrect paperwork as a reason. While doing their own digging, the team suspects that the police director is corrupt, but are more surprised to learn it's actually their Bulgarian liaison. While she doesn't explicitly know where Shaw's "playhouse" for punished girls is, she does provide them with the house leader's identity. Forrester tasks Raines with keeping tabs on a volatile Powell, who struggles with past experiences tackling a sex trafficker in Bolivia. He oversteps when he assaults Shaw in an interrogation room, and the Bulgarians threaten with disciplinary actions. Smitty however manages to negotiate a deal which clears Powell of any wrongdoing.

• This is the second episode where Jeremy Sisto (Jubal Valentine) isn't credited as a Special Guest Star. Instead, he appears under the list of Guest Stars for the episode, receiving the "And" credit.

Disgraced former US Secretary of Energy James Gaddis is arrested by Austrian police in Vienna on suspicion of peddling classified gold bars. The Fly Team arrive to assist the US embassy with the investigation, and learns that the bars were payment in exchange for handing classified nuclear documents to Iranian intelligence. Forrester goes undercover as a computer expert to assist Gaddis and the Iranian operative with removing the documents' redaction, but the team find cause for alarm when his GPS is deactivated when he and Gaddis are brought to a warehouse. However, Vo and Raines manages to deduce the area from CCTV footage and rescue Forrester and Gaddis, the latter turning on them last second. Additionally, Forrester has Powell benched for his behaviour in Bulgaria, but later finds himself offering him an undercover assignment in Germany to make ends meet. The mission is disrupted by an Iranian defector who was also tracking the operative, but Smitty finds a way for him to assist them and later give him clear passage in return.

• This episode marks the final appearance of Greg Hovanessian (Damian Powell).

Allie Baker, an American student, reports that she has been raped to Czech police in Prague, but is arrested after seemingly attacking the officers. The Fly Team head there and learns that she will be charged with assault on the officers and her rape case being dismissed due to lack of evidence, and furthermore for harassment after publicly revealing the officers' identities on social media. Forrester however manages to ensure that the latter charge is dropped. Vo leans on her military experience handling rape victims when getting through to Allie. The team begin to gather evidence which leads them to a Dutch linguist who is wanted for 18 other rape cases in Central and Southern Europe. The team head to Bratislava, his latest location, and work with Slovak police in an undercover operation to secure evidence against him. Vo goes undercover, but at a party, he switches victims last second before his arrest. The team and the police question him under the guise of drug charges in order to get a confession out of him.

Henry Dawson, the young son of Eli and Brianna Dawson, is abducted from a bunker at their new family home in Tuscany, Italy. The Fly Team work with the Italian police in locating Henry, but the matter is complicated when the anti-mafia suspects mobster Marco Banchero is involved. The family decides to pay the ransom in exchange for Henry's return, which the team manage to secure enough funds for through Banchero's American assets and hidden money in the bunker; but Banchero goes back on his word. The anti-mafia commissar decides to kidnap Banchero's grandson in order to increase pressure on him, which the team are strongly against. However, they eventually figure how to use the commissar's strategy in their favour without actually kidnapping the grandson, with the help of AI, to make it seem like the grandson was kidnapped. Banchero relents and releases Henry, who is eventually returned safely to his parents. Tate makes a visit to her ex-husband in order to meet her daughter again.

• Jeremy Sisto (Jubal Valentine) is credited as a Special Guest Star.

Jubal Valentine heads to Budapest to assist the Fly Team and the CIA in taking down Byron Molina, the nephew of Durango cartel leader Antonio Vargas, who specialises in illegal weapons with Antonio having been responsible for ordering a series of attacks against Jubal and his colleagues in the FBI's New York Field Office three years ago with one incident resulting in the death of Jubal's girlfriend, Rina Trenholm. The CIA asks Forrester to go undercover as a weapons expert to assist their informant, Gabriel Fuentes. The team is however surprised to learn that the agency has no intention of allowing the cartel to be arrested and prosecuted, but killed by drone, which they strongly oppose. As the deal between Molina and an Austrian buyer goes down, Forrester realises that a girl who accompanied Molina will be a civilian casualty unless she can be extradited from the location, however the CIA remain adamant about intervening until the last second before the missile is dropped. Fuentes is killed in the ensuing struggle, while Molina remains heavily wounded, but survives and is apprehended. The CIA representative indicates that the Durango cartel was only the beginning for their new strategy abroad.

• Jeremy Sisto (Jubal Valentine) is credited as a Special Guest Star.

Raines and Tate are dispatched to the Western Romanian border to extradite The Chain Cutters right-hand-man Tyler Selvidge in return for information on his group, who are claiming to combat child trafficking. However, the guard post is ambushed leaving three guards and Selvidge dead and one guard injured. The duo stumble upon the leader, Sam Keaton, who was looking for Selvidge. He pinpoints that Xavier Lee, one of his own men, has gone rogue and is seeking to sacrifice a little girl for a religious calling. After a shootout with the Romanian mob, they take him to a village, where Raines fights Lee at the village church where the girl is kept hostage. Tate, who was injured but is now patched up, manages to kill Lee before he can activate the bomb strapped on the girl. Together with Romanian police, they return the girl to her parents. Following the mission, Raines begins to consider there exists a higher power.

Maritime security contractor Ryan Karloski is found murdered in his hotel room after a wild night out in Amsterdam's red light district. The team works with Dutch police to identify the killer but find themselves going against Karloski's friends when they take matters into their own hands. The crime scene is also revealed to be staged and evidence points back to his friends and the ship they work on. They learn from his uncle that he sought legal advice from him about witnessing human trafficking on the ship, and one his friends, Bernard Almaz, is revealed to have handled people on the ship and killed Karloski for knowing too much. With help from one of the ship's victims, the team apprehend the captain as well for leading the operation. Raines substitutes for Tate when she shifts focus on a custody battle of her daughter with her ex, which threatens her relationship with her daughter. She initially resigns from the team, but Raines secures her a specialised passport which will protect her from judicial persecution.

• This episode marks the final appearance of Luke Kleintank (Scott Forrester).