After Rina is critically wounded while heading to work with Jubal, the team makes the chilling discovery that a vengeful Vargas orchestrated the shooting from behind bars and continues to target the rest of their team and their loved ones.

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 (II) and FBI: International S01E01 Pilot (III).

When a young couple is found murdered in a New York City park after returning from vacation, the team searches for a suspect linked to the drug trade. Also, Scola turns over a new leaf when it comes to his relationships.

OA is forced to confront one of his biggest fears when the team discovers that deadly sarin gas may have been sold to terrorists.

The murder of a TSA agent leads the team to hunt down a killer who is using drug mules to exploit airport security checkpoints. Also, OA struggles to cope with the aftermath of the sarin gas exposure and the 10th anniversary of his army friend's death in Afghanistan.

After a suburban woman is kidnapped from her home, the team looks into trysts on both sides of a seemingly perfect marriage. Also, OA feels pressure from Mona to make changes in his career path.

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, OA and the team must stop a hacker who is disabling life-saving equipment in several New York City hospitals. Jubal's son waits for important surgery at one of the impacted hospitals.

The team must track down a shooter targeting detectives from the same precinct and unit, while facing mounting tension from the NYPD. Also, Tiffany finds that her NYPD roots may be influencing her view of the situation.

After a young girl is kidnapped from her daycare, the team must help her parents navigate a debt owed to the deadly gang in their neighborhood; Maggie struggles to focus on the case when her sister returns from rehab.

The team searches for an abducted college coed; Jubal has a tense encounter with Rina's mother.

The team finds a connection between bombings and a private veterans' club in New York City; Isobel tells a reluctant OA to recruit a former Army buddy for intel.

The team hunts for a serial killer who is targeting young, homeless men. Also, Tiffany and Scola don’t see eye to eye on how to handle the case or the difference between partners and co-workers.

Maggie goes under cover working in a bar to investigate an anti-government group that regularly gathers there; a single father on the periphery of the group begins to fear he's in danger of becoming collateral damage.

The team realizes they have a cross-country serial killer on their hands; the case has ties to Isobel's father, Robert, and his hotel, leading to revelations about their fractured relationship.

After an immigration agent is fatally shot at a hockey game, the team attempts to find the shooter, who they believe may also be targeting Congressman Curtis Grange, who was at the same game.

When a morning show host is murdered inside her home, the team tracks the killer, who they realize is targeting powerful women. Also, things become awkward for Scola when Special Agent Nina Chase becomes part of the team during Maggie's recovery.

As the team investigates a string of jewellery store robberies that culminate in a double murder, they uncover a connection to a 16-year-old boy trying to survive the foster care system. Tiffany becomes personally invested after learning about the boy's ill-fated upbringing.

The team investigates an extremist gun group after an anti-gun lobbyist building is bombed; SAC Bashar dangles a possible promotion for OA.

When a retired DEA agent is shot outside a bakery, the team works to determine if the victim’s past cases or current bouncer job are connected to the murder. Also, Nina and Tiffany clash over the use of an informant while they are paired during the investigation.

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.