When a bus explosion kills several people, the team races to prevent future attacks and stop the person responsible with the ensuring investigation later resulting in the death of fellow agent Trevor Hobbs. They determine that the attack is linked to a Somali terrorist organisation, Al-Shabaab, and that the attacker wanted to draw attention to the US's involvement overseas. However, whenever they think they're getting closer to the attacker, he slips away in many ways, before finally losing their tail at the memorial for 9/11. Hobbs' death takes a toll on Tiffany, who becomes determined to find the attacker, but is disappointed when they're unsuccessful. Scola finds himself trying to balance life as a father and an FBI agent. The team later holds a memorial ceremony in the lobby of 26 Fed where everyone shares their memories about him with OA even revealing that after Hobbs told him on the first day they met he wouldn't be able to remember OA's full name, Hobbs gave him his nickname.

When the president of the New York Federal Reserve Duncan Martin, is murdered by seemingly trying to be a good samaritan, the team investigate and soon find themselves racing against time to not only apprehend the suspect but also save Gabby Martinez, the younger sister of Jillian Martinez, both of whom went missing eight years ago and were presumed dead. Jubal takes a personal interest in the case, knowing that he originally investigated the sisters' disappearance. Once they corner the suspect and Gabby in a store, the situation turns on its head when Gabby shoots the suspect and makes one last stand herself before her father assists in talking her down while Jubal later shoots the suspect when he tries to kill Gabby. Jubal also deals with the news that his son, Tyler has been suspended from school after being caught drinking. He is later tasked with taking him to therapy, and assures him that everyone makes mistakes, and what matters is what happens next, repeating what Maggie said to him earlier.

Local bar owner Eric Cantwell is abducted and later dies of his injuries, leaving the FBI with a clue of Russians being behind his abduction. Investigation reveals that he and his partner were in debt to a Ukrainian club owner and his enforcer Viktor. Since neither of them paid their debts, the FBI's theory is that Viktor was sent to kill them. OA is shocked to learn that his new love interest Gemma, frequents the club and worries that she is involved with the wrong crowd. The team takes one of her friends as an informant, who is aided by Tiffany undercover. Their mission takes on uncertain tension which causes mild suspicions in the club. However, the mission goes awry after the friend wakes higher suspicions by the Ukrainian, but he and Viktor are swiftly apprehended as they try to kill them. Just as OA prepares to discuss Gemma's lifestyle with her, they learn that her friend died of her injuries.

Federal judge Charles Pollan is killed in broad daylight, and a quote from his killer leads the team to the local Islamic center, where they encounter undercover agent Hassan Khalil. It's revealed that Khalil is working with Maggie's former Quantico mentor, Jessica Blake, on taking down an Islamic terror cell, which the killer, is suspected of being involved in. OA finds the case complicated with Khalil's approach to the killer, identified as Adil Kazem, thinking he could have gone too far. Khalil goes undercover again to receive Adil's mission as a new member of the cell, but the mission goes awry when Adil shoots him at the targeted ceremony. He is hospitalised after he saves OA from Adil. OA reports him to the OPR after learning that he had essentially radicalised Adil for the purpose of using him to infiltrate the cell. Additionally, he tells Gemma the truth about the mission that killed her friend, after which she demands him to leave.

• Charlotte Sullivan (Jessica Blake) is credited as a Special Guest Star.

Migrant center director Matthew Sawyer is abducted while leaving work for the night. Initially the FBI suspects a man who had harassed him and the center, but his alibi checks out. They track the abductor's car back to Sawyer's home, where a hostage situation ensues. It's revealed that the abductor, former Mexican cop Hector Ramirez, suspected Sawyer of kidnapping his daughter Maria. The team rush to locate his daughter and defusing the situation, with Maggie letting herself be taken hostage in return for Mrs. Sawyer's release on medical grounds. Scola and Wallace locate the real kidnapper, Jared Gamble, who explains that he didn't intend on kidnapping Maria, but despite this, he resists and is shot and killed. However, they manage to locate Maria in his basement, just as OA and SWAT storm the Sawyer residence to save Maggie. Maggie confides in Blake about the hostage situation and understanding the role of parenting.

• Charlotte Sullivan (Jessica Blake) is credited as a Special Guest Star.

Angela Lane, an employee with the Bureau of Land Management is sprayed with ricin gas on the subway and dies shortly after. Another woman, Sharon Williams, who worked as a lobbyist for fracking company Green Solutions, also succumbs to the poison. Evidence leads them to a group of conservationists, where two members, Landon and Anthony, decided to resort to violence for the cause. With Landon in custody, the team rush to stop Anthony from poisoning a state senator opening an oil refinery. A third attack happens, but the victim survives, who is revealed to be the sister of the governor's policy advisor. The last suspect is identified as the boys' professor, who releases ricin through the sprinkler system at Green Solutions, but Maggie and OA manage to deactivate the system and apprehend her just as everyone is evacuated. Blake collapses during the search of Landon's house and is hospitalised with an aneurysm and later dies during surgery. Having considered IVF to have a child herself, Maggie now faces the prospect of looking after Blake's young daughter, Ella.

• Charlotte Sullivan (Jessica Blake) is credited as a Special Guest Star.

Castille is injured during a bombing of a restaurant, which claims the life of congresswoman Carol Jones. The bombing also claims the life of a boy living in the same townhouse as her. The bombing leads the team to an anarchist chatroom, where they identify the user supplying the bombs to be a Russian agent working at the consulate, Marina Kostova. The State Department however warns them to not arrest her due to an ongoing prisoner exchange, despite evidence suggesting Kostova's involvement. The team rush to stop another bomb, which is identified to be planted at an expo center where a right-wing alliance is meant to hold an event. Maggie sneaks under the stage to detail the bomb for Ian, and they stop Kostova's companion from detonating the bomb. Kostova herself is later arrested after leaving the consulate. The State Department informs Castille that the American prisoner was killed shortly after Kostova's arrest. Maggie settles in trying to take care of Ella, while OA and Gemma figure out how to move forward with their relationship.

Military weapons dealer James Sun is shot and killed during a purchase of RBX explosives. The team swiftly identify the buyer and he confesses to the murder, but also provides them with a buyer for the RBX. Scola and Tiffany meet the buyer undercover, and learn that he is buying the explosives on behalf of Al-Shabaab. Tiffany sees someone resembling their ringleader, Hakim Siran, despite reports that he is in Africa. Her guilt over Hobbs' death affects her work as she begins to insist on finding Siran after his supposed sighting, derailing the operation after her and Scola's covers are blown and a chase ensues with the buyer. However, before they can receive a confirmation of Siran's presence in New York, the man dies of his injuries. Castille questions Tiffany's state to be in the field just as the team are informed that Siran re-entered the US a week before. Tiffany's efforts to assure Hobbs' wife about capturing Siran falls on deaf ears, as she tells her that she has moved on, and she should do the same.

Retired FBI agent Mike Rosen is abducted, tortured and killed after being forced to provide a group of robbers the location of a diamond transport from his security firm. The team disable one and later another robber who briefly escapes, and link his identity with the Perez brothers, who deals with diamonds. The case is complicated when they apprehend Samuel Jacobson, who is an informant for Stuart's girlfriend Nina Chase. Through Jacobson, Stuart and Nina go undercover as a couple looking for diamonds and ensure a deal at a Manhattan apartment with Beto Perez. When Nina goes out to look at the remaining diamonds provided by Beto's brother Carlos, an NYPD patrol unit pulls in and spooks Carlos, forcing her to tackle him as the officers, OA and Tiffany arrive on scene. Stuart and Maggie meanwhile tackle Beto when he becomes confrontational. Throughout the mission, Stuart clashes with Nina on the risks of them doing it together, expressing a preference for a safer approach. In the end they agree to stand in things together.

• Shantel VanSanten (Nina Chase) is credited as a Special Guest Star.

Off-duty FDIC security guard Will Douglas is killed when checking up on a suspected domestic abuse after visiting a date. The team learns that the victim of the suspected domestic, Denise Mamet, was the surrogate mother of the Webb family, who were forced to give up her address. Furthermore, Mamet is pregnant and the daughter of Secret Testament cult leader Aaron Mamet; and follower Travis Keating abducted her for the purpose of cleansing her. The team works with the ATF to ensure Denise's extraction, but the operation complicates when Maggie alarms the cult, with the women and children shielding the armed men. OA chases Aaron into underground tunnels and convinces him to order his men to stand down, clearing the path for Maggie and Scola to free Denise. The operation takes a toll on Maggie, making her worry about Ella becoming orphaned should something happen to her. OA advises Castille to request that she take maternity leave, after Castille initially expressed for him to make an evaluation of her ability to work.

Tyler Combs, the protege of tech mogul Leo Grant is abducted by armed men and forced to reveal the location of Grant's meeting with representatives of the Taliban — a meeting arranged by the State Department to negotiate rare earth metal mining rights with the Afghan government. Taliban leader Abdul Sayeed is abducted by the men, and the FBI traces a discarded flashbang to dentist Michael Garrett, who reveals his son James is being held as a prisoner-of-war in Afghanistan, and Sayeed has been taken by his son's old unit to force a prisoner exchange, which the Taliban have agreed to. The team locates the soldiers, and OA tries to negotiate rather than breaching the hideout as ordered. Sayeed attempts to escape and is killed, leaving them with no exchange for Garrett. Using deepfake, the team convinces the Taliban to release Garrett, although the news of Sayeed's death leaks and a shootout ensues, with OA managing to rescue Garrett. OA's relationship with Gemma faces challenges of openness, and he later manages to open up to her about a past captivity.

Truck driver Tim Baker is killed in the Jamaica Bay Wildlife Refuge and the team learns that he was transporting fentanyl, with half of the batch missing. They later discover them disguised as oxycodone pills, which a group of girls overdose upon in a night club. Jubal is surprised to learn that his godson Nate Becerra supplies the girls with the pills, and becomes caught between his duty as an agent and loyalty to his friend and former agent, Jose Becerra, after a bag of pills is discovered in Nate's room. Once he convinces Nate to help the team, they track down his supplier, who sets Nate up with his subsequent source, Long Island biker gang leader Gio Russo. Jubal joins Nate undercover, but he accidentally blows their cover and a hostage crises ensues. OA ensures that the demands are met, but Jose intervenes and Nate is shot in the struggle. Although Nate survives, Jubal and Jose's friendship tanks, as he blames him for Nate's fate.

Maggie returns from maternity leave as the team investigate the death of truck driver Lucas Chandler, but his cargo has not been stolen. A woman perishes when her car explodes, and Chandler is revealed to have been a new identity for former soldier Nick Ward. Both of whom they learn worked for the CIA, and that crates of thermal grenades were actually stolen from Ward's truck. The factory head of the weapons producer is also murdered, of which the lead points to Al-Shabaab. The team ransack two buildings belonging to the group, one proven empty and another with members who refuse to give them any further information about the pending attack. However, an image from their storage room points the team to an event where representatives of the Somalian government are scheduled to attend. The attack goes ahead as they arrive, but they stop both Hakim Siran and his associate before more harm can be done. Despite being rejected by Hobbs' wife earlier, Tiffany informs her of Siran's fate, giving herself closure over Hobbs' demise.

• This episode marks the final appearance of Katherine Renee Kane (Tiffany Wallace) in the opening credit and also as a series regular.