After a bomb explosion devastates a residential apartment building, special agents Maggie Bell and Omar Adom “OA” Zidan of the New York office of the Federal Bureau of Investigation investigate a possible war between rival gangs – that is, until their prime suspects are discovered brutally murdered.
When the son of a well-known retired FBI agent is taken just blocks from their home in what appears to be a revenge kidnapping, the team must uncover if it's tied to the agent's past or trouble the son has gotten into on his own. Also, Isobel must make a hard call when information from the past comes to light.
When the leader of a drug cartel and one of the world’s most wanted men, Antonio Vargas, is apprehended by the team, the entire FBI headquarters is put at risk when his henchmen unveil a terroristic threat to free him. During the turmoil, Isobel must make the difficult decision whether to sacrifice her conscience or her career.
When the CEO of a major brokerage firm is shot and killed while surrounded by protesters, the team looks into who had the most to lose from his company's perceived manipulations. Also, Scola's previous Wall Street career and the reasons he left come to light as the financial details of the case begin to unfold.
After a young woman is killed on her way home from a lavish yacht party, the team investigates who she was and how she came to be at the event, which was attended by some of the most influential people in the world. Also, Maggie brings Crosby into the investigation after a murder suspect is identified as a veteran who had been on several Army operations with Crosby. The crossover continues on FBI: Most Wanted S03E01 “Exposed (2)” and FBI: International S01E01 “Pilot (3).”
Maggie, OA and the team must stop a hacker who is disabling life-saving equipment in several New York City hospitals, while demanding a full investigation into the recently deceased patients of a local psychiatric facility. With Jubal’s son waiting for important surgery at one of the impacted hospitals, Jubal’s adamant about remaining involved in the case despite Isobel’s reservations.
After the team finds a connection between bombings at government agencies and a private veterans’ club in New York City, Isobel tells OA to recruit his former Army buddy, Chris, for intel since he spends time at the club. However, knowing the difficulty soldiers like Chris often face returning to civilian life, OA is reluctant to follow orders.
The team attempts to extract key information from a vulnerable 9/11 widow, Hannah Thompson, who is shocked that her new “boyfriend” is the manipulative leader of a terrorist group planning an attack. Also, Scola is reminded of his brother’s death on 9/11, and Tiffany worries about his emotional choices during the investigation
Maggie goes undercover working in a bar to investigate an anti-government group that regularly gathers there and has several members suspected in a series of bombings. The case opens old wounds for her when a single father on the periphery of the group begins to fear he’s in danger of becoming collateral damage.
When a Muslim college student and his younger brother are murdered, the team connects with the outraged imam of OA’s former mosque, who insists the victims were wrongly targeted as terrorists. Also, OA must reconsider where his loyalties lie when working the case with a Muslim anti-terrorist agent bent on solving the investigation through any means necessary.
After the president of the NY Fed is gunned down trying to help a young woman in peril, the team races to find the killer and the missing woman. Additionally, a distressing connection to one of Jubal’s past cases is revealed during the investigation, compounding the pressure on him as he also deals with his son’s school suspension.
When a retired FBI agent is tortured and killed while working a security job, Scola and Nina go undercover as a married couple deep in the diamond game as the team tries to find out who is responsible. During the course of his and Nina’s dangerous assignment, Scola is plagued by the possibility that their son Doug could end up parentless.
The team is thrown into a highly political case after four members of the Taliban are shot and one is kidnapped in New York with no record of their entrance into the country. Having served in the U.S. Army, this case hits close to home for OA, who struggles to open up to Gemma about his past in Afghanistan.