Special Agent Scott Forrester and his Budapest-based FBI fly team head to Croatia, after Isobel Castille enlists their help to capture an American fugitive who escaped to Zagreb with a 14-year-old girl. OA continues with the mission overseas, intent on bringing the fugitive to justice, while Europol agent Katrin Jaeger attempts to help the team secure the necessary support and access from the less-than-cooperative local authorities. The crossover starts on FBI S04E01 “All That Glitters (1)” and FBI: Most Wanted S03E01 “Exposed (2).”
After a U.S. intelligence negotiator goes missing and her ransacked Paris apartment is discovered to be covered in her blood, the team is on the clock to find her before the country's nuclear secrets fall into the wrong hands. Also, Forrester finds himself drawing certain parallels to his mother's disappearance.
When a notorious American tech tycoon becomes involved in a murder in Frankfurt, the Fly Team must chase him down amid the local protesters he’s incited with his conspiracy theories on social media. Also, Jaeger relishes working in her home country, and Forrester must make a decision involving his mother’s past.
When a couple flees to Albania while awaiting sentencing for bilking millions in COVID relief funds from the U.S. government, the Fly Team and Jaeger must contend with the wife’s menacing crime family as they try to track the duo down. Also, Kellett works the case from Budapest as she and Forrester try to regain their professional boundaries.
The Fly Team is called in to investigate when an American college student is arrested at a hostel in Prague for showing aggression toward local police who were dismissive of her sexual abuse claims. Also, Vo makes use of her sexual assault advocacy experience from her army days as they work to ensure the victim gets justice.
When a U.S. mercenary claiming to fight child trafficking abroad is apprehended at a remote Romanian border police outpost after the U.S. DOJ suspects his crew of embezzlement, Tate and Raines attempt to get him to flip on the leader of the group. The mission takes a turn when the outpost is attacked as they work to secure evidence.
When a former member of the Irish Republican Army turned U.S. citizen is shot while in London with his son touring youth football academies, Smitty and the Fly Team work to hunt down the people responsible as the group becomes increasingly violent. While in London, Smitty pays a visit to her mother who she believes can help the team locate an old family friend who may have a connection to the case.
When a Russian biochemist is assassinated for trying to defect with his highly sensitive biotoxins research, the Fly Team springs into action to protect his daughter, whose father’s last wish was that she get his research to a trusted American microbiologist. Meanwhile, Mitchell stays behind to help Vo during her recovery, and Booth clashes with Smitty when he finds out she could jeopardize his promotion.
The Fly Team leads an international manhunt when an American woman and her new husband flee from Baltimore to Istanbul with her young son after a heinous murder. Also, Vo partners up with Special Agent Riley Quinn, who was not only sent to Budapest to work her first big case alongside The Fly Team but to also clandestinely investigate a member of the team.
When an American businessman is gunned down in Bratislava, the Fly Team must work with an unscrupulous local detective while safeguarding the sole witness, a fearful tourist from Wisconsin being held by police. Meanwhile, Quinn begins to feel pressure from her brother to deliver information on Mitchell.
After a young American woman is brutally murdered in Venice, the Fly Team is met with hostility when they discover that their person of interest has ties to a well-connected Italian family. Soon, the case gets even more complicated when the CIA Station Chief shows up with an agenda of his own. Meanwhile, pressure mounts on Quinn to deliver intel on Mitchell.
When a televangelist on the FBI’s most wanted list surfaces in Gibraltar to seek asylum, the Fly Team’s attempts to take him down hit a roadblock as they face political stonewalling upon arrival to the region. When the predatory preacher goes after the daughter of a disciple as his next target, the team must abandon protocol to intervene.
The Fly Team heads to the country of Georgia to determine the motive behind an attack that targeted two American soldiers at a NATO-Georgia joint training center before it turns into an international incident. Meanwhile, a supervisory position opens in another FBI division in Europe, and Mitchell encourages both Vo and Raines to apply.
When a suspected American arms dealer with a lengthy rap sheet pops up in Vienna with stolen weapons, the Fly Team sends Mitchell and Smitty undercover to try to infiltrate his operation. During the mission, Smitty enters muddy waters while working with the suspect’s wife. Meanwhile, Mitchell’s biological father shows up in Budapest after being released from prison to seek him out despite Mitchell’s disinterest.
When an American official in charge of a high-profile three-way prisoner swap in Belgrade is detained in Romania, he requests the Fly Team step in and carry out the exchange. When their convoy is attacked and one of the prisoners escapes, the team must do everything in their power to find the missing prisoner before the highly sensitive mission is compromised.