As the new season of this totally re-imagined show opens, Martin Odum is a fugitive, hiding out in present day London and wanted by the FBI for a crime he did not commit. He can't remember his life prior to an injury he suffered in the Iraq War, so he's searching for clues about his true identity with the help of CIA agent Nina Brenner. Meanwhile, in 2001, FBI agent Curtis Ballard and his Czech Police partner, Gabi Miskova, launch an investigation into a Russian gangster named Dimitry.
In present day London, Martin is finally able to make contact with Ilyana Crawford, a woman who may be linked to his past. Unable to get answers from her, he turns to her teenage daughter, Kate, who is in search of her own identity. In 2001 Prague, Dmitry is on a mission to locate a wanted war criminal believed to be connected to the Chechen gangsters. But Dimitry's handler is concerned that his infiltration techniques may be crossing the line.
It's a race against time as Martin searches for Kate in Paris. He's convinced the peaceful protest she's attending may turn violent at the hands of her friend Ifti, a boy with radical beliefs. In 2001 Prague, Dmitry discovers that the key to getting close to Doku Zakayev may not be his brother Tamir, but instead Doku's wife, Ilyana. In 1991 Lithuania, a younger Ballard is involved in an incident that will affect the rest of his life.
In present day Paris, Kate is a fugitive as a result of her link to a violent attack. Martin puts her into hiding and attempts to use Nina to get Kate out of trouble. Meanwhile, Ballard learns some useful information from Ilyana that could lead him to Martin. In 2001 Prague, when Ilyana asks Dmitry for a dangerous favor, he offers her a deal instead. And Tamir tries to save his own skin by using evidence that could help Ballard and Gabi finally nail Dmitry.
In present day Paris, Nina and MI6 agent Simon Hardy offer Kate a deal that Martin doesn't like, but Martin may not have a choice. Ballard convinces the FBI to let him take down Martin. In 2001 Prague, Dmitry enlists Ilyana as an MI-6 operative and gives her an assignment. In 1976 England, we learn that Terrence has a secret life.
In present day Paris, Martin prepares Kate for a dangerous job that Simon isn't sure she can handle. In Prague, Gabi confronts the intelligence agents about Martin Odum. She knows they're hiding something. In 2001 Prague, Ballard and Gabi discover Dmitry has a vulnerability. In 1984 England, Alex is recruited for a distinguished position, but finds that it comes with a demand for a personal sacrifice.
In present day Prague, Kate goes missing, and Martin fears she's been abducted. Martin makes a risky proposition to Nina and Simon in an effort to bring her to safety. Gabi discovers that Blazek may have a dangerous connection to Tamir. In 2001 Prague, Ballard and Gabi use questionable methods to threaten Dmitry. In 1985 England, Alex suspects his friend Terrence has resorted to ruthless tactics.
In present day Prague, Martin goes back to work for Tamir, just like he did in 2001, but Tamir has other plans for him. Gabi confronts Blazek about his secret dealings. Kate is a prisoner in the President's compound in Chechnya. In 2001 Prague, Dmitry must convince Tamir to pick up where Doku left off and earn General Arsanov's trust. Ballard and Gabi suspect Dmitry and Ilyana have conspired to commit murder.
Martin and Nina search for Tamir's associate in hopes of getting some answers; two Chechen assassins put a deadly plan into action; Malika gives Beslan orders; in 2001, Dmitry struggles to complete his mission.
In present day Prague, Martin makes a deal with the Russians to rescue Kate. Meanwhile, President Arsanov's plan for Kate is moving forward in Chechnya. Gabi struggles to decide what to do about her husband. In 2004, Dmitry asks one last favor of Terrence. And in a flashback to 1972, the last pieces of the puzzle to understanding Martin Odum's true identity are revealed.