When a psychologist with national security intel goes missing on a hike in the Swiss Alps, the Fly Team works alongside a friendly face, Agent Tyler Booth, to find him. Meanwhile, Mitchell receives unnerving news regarding his biological father.

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.