After a federal judge disappears, a routine investigation takes a dark turn as the team uncovers that the judge had been searching for his missing son on a secluded island on the city's edge, where authority has crumbled. Meanwhile, reality weighs heavy on Jubal as he takes on a new leadership role.

After Jubal narrowly escapes a calculated assault on a secret FBI office, the team discovers a rogue terrorist group has infiltrated the FBI. Unsure of who to trust, the team must work in the shadows to unmask the culprits threatening the sanctity of the New York field office.

Maggie and Dana struggle to find justice for victims murdered by a serial killer who left a ghoulish mark on all of his victims, while the mayor limits the investigation in order to prevent economical loss.

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.

When a passenger train is hijacked and rerouted while at high speed with an unarmed OA and Gemma on board, the team races to wrest control away from the unhinged perpetrators and prevent a catastrophe.

When a CEO is killed by a targeted explosion inside his penthouse, the team must work to figure out how someone accessed the highly secure building. Their task is further complicated when they discover the crime may be the work of an artificial intelligence program. Meanwhile, Maggie pumps the brakes on her personal life.

A woman with information about the death of Maggie’s husband is abducted, leading OA and the team to uncover a criminal operation larger than anyone imagined. Also, Dana puts her career in jeopardy when she stands by and allows Maggie to work on this case that has such a personal connection to her.

A car crash results in the death of a photographer; Maggie sympathizes with his widow when she notices similarities with her own husband's death.

After a truck filled with armour-piercing rifles is hijacked, the team works to discover who stole it, and what they have planned for the stolen weapons. A friend from OA's past returns to help with the case, but OA isn't sure he can trust him.

After the police ignore a desperate father's plea for help, he abducts a billionaire's daughter and holds her hostage in a near-impenetrable safe room until his own missing child is returned to him. Also, Jubal puts his hostage negotiation skills to the test.

Jess LaCroix and his team come to help OA find a fugitive LaCroix arrested years ago after a bus with 26 students goes missing and he's the main suspect. The crossover continues on FBI: Most Wanted S01E09 Reveille (II).

The FBI team investigates a drug deal gone bad after the body of a college student is found. Also, Detective Hailey Upton temporarily joins the team and finds her usual investigative methods clash with the Bureau's more buttoned-up environment.

The team races to stop an active serial killer after three women are found weighted down at the bottom of a lake, and Jubal looks into an old closed case after there are multiple similarities to the recent victims.

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.

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).

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.

The team jumps into action when analyst Kelly Moran is taken hostage.

Jubal's longtime confidential informant brings intel of an impending large-scale terror attack to the team, but when the details don't add up, Jubal must sift out the truth from a man who's known him at his worst.

After a key witness and a U.S. marshal are ambushed and killed, Maggie and OA must track down a man who leaked the information that led to their murders.

After an investigative journalist is murdered, the team uncovers information linking the suspect to past cases. The victim’s death also strikes a chord with Maggie, leaving her desperate for answers in regard to a traumatic event in her personal life.

An American diplomat is killed while being used as a pawn in a dangerous drug ring, and the team must work together to bring them down. Also, Jubal and OA try to help friends from their past fight off their inner demons.

The son of a retired FBI agent is kidnapped, and the team must investigate if it's an act of revenge; Isobel must make a hard call when information from the past comes to light.

When five prominent men are killed at a trendy New York City restaurant, the team’s investigation brings them into contact with a lieutenant in Antonio Vargas’ cartel, triggering a long-awaited showdown between Isobel and Vargas.

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.