Following a pursuit of a group of robbers in Los Angeles which leads to his partner being hospitalised, supervisory special agent Wesley "Wes" Mitchell heads to Budapest and continues the investigation into the robbery crew with the Fly Team. But with two of the robbers most likely killed, the team and Mitchell rely on information from the surviving member, Vilmos Barany, who reveals that Greg Czonka, a dual citizen who runs a youth centre, recruits boys from his centre to conduct robberies on his behalf, with further evidence pointing to a remitting scheme. Mitchell's unofficial visit to Czonka puts him at odds with Hungarian police and a reprimand from Vo. Mitchell later learns that his partner died from complications during surgery, and the case claims a further victim when they learn that an embassy counsellor was on Czonka's payroll. As Czonka is arrested, he vows to get back at Mitchell. With his relationship in shambles, Mitchell is offered to work with the Fly Team by Vo, who views him more qualified then their current leader, an offer Mitchell is left to consider.

With Mitchell taking over as the new Fly Team leader, the team are dispatched to Rotterdam to assist the Dutch police when the US Ambassador to the Netherlands Arthur Coates is taken hostage at the World One News TV station along with 60 civilians. The crew demands a transfer of €40 million and a helicopter in exchange for releasing the hostages. The team learns that imprisoned businessman Clemens Anholts masterminded the plot through secret messages to retrieve the location of the key witness against him for the murder of his ex-girlfriend, from the ambassador. Once the hostages are freed and the crew apprehended, the Fly Team go rogue to secure the witness, guarding themselves against police on Anholts' payroll. Mitchell fends her off from a hitman, but is wounded in the process, but nonetheless manages to keep him at bay until the Fly Team and Dutch police arrive. The conviction against Anholts is retained as he is extradited to the US, while the witness is put in witness protection until she can testify.

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

Seventeen-year-old Leah Cardwell is abducted while out on a beach party in Lisbon, Portugal. The Fly Team joins the Portuguese police in tackling the investigation, but less then 24 hours after Leah was abducted, she is found alive and well, further revealing that she was let go after the kidnapper heard her mother's vows in the news. The case takes an unusual turn when they begin to doubt Leah's story, suspecting the entire abduction could have been staged. Though they are able to confirm her story, a closer look at her parents' history reveals that her father most recently secured custody over her two brothers and Leah is scheduled to take her father's surname once she turns eighteen, and he most likely hired the kidnapper to make the mother look bad. This is further proven when the father officially submits a child negligence complaint. Mitchell and Vo force the father into a corner, leaving him no choice but confess or risk prison time in either the US or Portugal.

The Deputy Inspector General approaches the Fly Team with a special assignment to investigate corrupt DEA agent Daniel Lopez operating in Madrid, Spain, and more specifically asking Tate to work undercover with her skillset; to get him to implicate himself. Though hesitant at first, Tate accepts the assignment. The team arrives in Madrid under the guise of assisting the DEA in their drug investigation into the Serrano cartel, whom they discover Lopez is working with. Tate joins Lopez in speaking to his informant, but quickly deduces that it must be someone else. Without informing Lopez, the team apprehends the real informant and turn him against Lopez and set up a bait for him about a false raid. But the cartel sees through this, leading to Tate's cover being blown after she visits Lopez prior to his meeting with the cartel’s attorney, but the team rapidly come to her rescue. The team convince Lopez' corrupt colleagues to turn against him, securing the conviction against him.

Delawarean Gil Schrader arrives in Warsaw, Poland, to meet Natalya Kovalenko, a girl he met on an online dating site, only for them both to abducted shortly after meeting each other in person. The Fly Team arrive to assist the Polish police in the case, but find their resources stretched thin. Schrader's abduction is revealed to be a part of a dating scam and that Natalya was in on the plan, but once apprehended, they convince her to cooperate to bring Schrader back. But with his bank accounts frozen by his daughter, the scammers force her to pay for her father's return. Through a middleman, the team and police find and free Schrader, but Smitty vows to save British national Keith Edmunds who also fell victim to the scammers and whose finger they found at Schrader's abduction site. The team decides to support her effort and together they head to Edmunds' last known location and fight through shooters before managing to free him.

Twelve American volunteers for the charity organisation Guided Hand are abducted in the high Atlas Mountains in Morocco and the Fly Team are dispatched to assist Moroccan police with the case. They learn that a checkpoint guard had gone back on his deal with Guided Hand founder Emmy Devlin, who is later found alive and well in another city. Furthermore, the abductors are revealed to be led by a Russian mercenary with a history of kidnapping foreign volunteers in Africa. Through a random video, the team determine that Emmy's husband Mark was held in an old school, which is empty when they get there. However, further evidence points them to a compound where the hostages are being kept and the Russian has his base of operations. The team go in and rescue the hostages. Mark demands other civilians be released as well, forcing Mitchell's hand. Once the hostages are saved, both Mark and Emmy are sent back to the US due to their outstanding warrants for unpaid debts, fraud and other economic charges by the IRS.

Tyler Booth, an agent and an acquittance of Mitchell, convinces Kelsey Haskins, the ex-wife of traitor and blackmailer Ed Haskins, to assist the FBI in luring him out of Russia. He heads to Budapest to receive Mitchell and the Fly Team's help, which Mitchell accepts. But not long after they proceed with their investigation, they learn that Ed rather wants to meet Kelsey in Tallinn, Estonia. Booth and the team attempt to keep the operation covert, but the Estonian police uncover their operation and offers their discretion despite them not initially being informed. Booth and Mitchell manage to make Kelsey push forward Ed's arrival time, but to everyone's surprise, she joins him when he arrives, risking imprisonment herself once they're both arrested. Additionally with Booth's daughter targeted, the team convince Ed to save Kelsey from imprisonment in exchange for his material password. The deputy director offers Booth ninety days temporary work with the Fly Team until he can figure out his next assignment.

Vilmos Barany is killed in prison by Greg Czonka before he can testify against him. The Fly Team work with the Hungarian prosecution to salvage the case against Czonka. During trail, Czonka's defence attempt to use Booth's testimony to discredit Mitchell's integrity as an agent and he later takes the stand himself, realising Czonka is going after him personally. With Mitchell's credibility in doubt, the judge considers ruling in favour of Czonka, until the team identifies the prison guard who put Barany together with Czonka. He provides them with a recording of who contacted him, identified as Victor Stoll. But before they can apprehend Stoll, he commits suicide. The team uses Stoll's safe keep of transactions against Czonka, which implicates him in Barany's death. Despite receiving a new sentence, Czonka later escapes from his prisoner transport and a sniper injures Vo in the process. The team locate an airfield Czonka made, but he has left the country when they reach it. With Vo in critical condition, Mitchell vows to get Czonka even without the badge.

As the team search for Csonka while waiting for news on Vo, the case takes a turn when Raines is kidnapped.

When a Russian biochemist is murdered while attempting to defect with his highly sensitive biotoxins research, the Fly Team springs into action with Raines protecting the biochemist's daughter as she seeks to bring her father's research to a trusted American microbiologist while Mitchell stays behind to help Vo during her recovery, and Booth and Smitty clash.