After turning herself into the FBI, Alex is aggressively interrogated to confess about who really bombed grand central. New evidence is uncovered that might lead to Alex's freedom. Back at Quantico, the group investigates serial murderers.
At Quantico, the NATs are given a long weekend off for New Year's Eve. Alex, Natalie, Shelby and Nimah, all fleeing from family problems, try to spend the weekend drinking and reviewing cold cases. Nimah tries to have a heart-to-heart with Miranda about her son's radicalization, with mixed results. In the present, Alex, Nimah and Natalie learn of Simon's abduction from a battered Elias, and find Simon with a detonator taped to his hand in the hotel where the Democratic delegates are staying. While Miranda works to defuse the bomb, Liam gets the delegates to the command center, where Senator Haas tells Shelby that she will ruin her for breaking Caleb's heart.
In the present, Alex is reinstated in the FBI. She and Natalie work together to prevent Natalie's death, even though it involves breaking the law. In the past, the trainees learn more about human intelligence.
At Quantico, the NATS team up for defensive driving lessons while tensions between Liam and Drew explode, resulting in shocking admissions and consequences. In the future, Simon grapples with his new reality in the aftermath of what's transpired.
At Quantico, the NATS are given a training exercise that hits too close to home for Shelby. While in the future, Alex finds an unlikely ally in Hannah, as she continues to try to stop the terrorist from striking again.
At Quantico the current assignment is to learn about human trafficking when Liam and Miranda challenge them to cross the U.S. / Canadian border without passports. Meanwhile, in the future, Simon continues to help Alex try to find the terrorist, but doing so puts his own life in great risk.
At Quantico, Alex, Shelby, and Iris soon learn some surprising truths about Drew, Will, and Caleb while investigating them for high-level security clearances. Meanwhile, in the future, Alex contacts Claire Hass in an attempt to locate her missing friends.
On career day at Quantico, the NATS meet with the representatives of various FBI branches. Meanwhile, in the future, Alex's search for the terrorist brings her into contact with some familiar faces, including one who knows the terrorist's endgame.
The NATS are excited that graduation is near as they prepare to leave Quantico and head out into the real world for their new assignments. In the future, Alex learns someone she cared about at Quantico is not who they seemed to be, as she finds herself at the heart of another possible attack.
The new CIA recruits begin running counter-surveillance ops at The Farm while Alex and Ryan navigate their new relationship with each other. In the future, Ryan and Raina try to disrupt the terrorists' plan to blend in with hostages.
The new CIA recruits continue training at The Farm focusing on assessment, while in the future, Alex goes undercover to infiltrate the terrorist group holding everyone hostage where she is shocked to discover not everyone is a stranger.
The recruits go through a training drill to test their stress levels; Alex attempts to gain information and get close to Owen; in the future, the terrorists make a demand that could possibly end the stand-off.
At the Farm, the trainees learn their next task is to decide on a drone strike, which triggers Alex's memories of Simon's sacrifice. Meanwhile, Shelby and Leon's relationship reaches the next level, and Nimah advises Alex and Ryan not to trust Harry. In the future, Alex questions if she can trust Lydia, leading to combat between the two.
At the Farm, Owen teaches the trainees about enhanced interrogation techniques, and turns the tables on his students by putting himself in the hot seat. Meanwhile, Shelby goes undercover, and in the future, a new president is sworn in.
At the Farm, Owen teaches the recruits a lesson on the necessity of betrayal, with a mission of getting the Venezuelan Consul to turn on his country. In the future, Alex teams up with Miranda to save the hostages, while President Claire Haas has a plan to end the crisis.
The recruits learn how to burn everything down if they're exposed. Meanwhile, a mysterious death leads to an FBI investigation at the Farm. In the future, Alex goes back into the perimeter and exposes the true traitor within the CIA.
In the wake of the G20 hostage crisis, President Claire Haas assembles an illegal and clandestine joint task force, bringing together Alex and her friends from both the FBI and CIA to unmask a global conspiracy.
While their newly appointed leader gets familiar with the team of CIA and FBI agents, Owen leads an investigation into the strange world of fake news. But hunting down the publishers of a fake story might lead to deadly consequences.
The whole team reexamines their personal connections, or more accurately, the lack thereof. Meanwhile, Alex forges an unexpected bond with an asset at the center of a conspiracy, and Harry struggles to find his place on the task force.
One of Alex's friends needs help when they're framed for a terror attack. With a vote in the House for Muslim registry bill, the Collaborators are stirring fear to pass the registry, our team heads to the Hill to turn the votes. Meanwhile, Alex and Owen track down an assassin.
Clay meets the President to discuss the future of the task force, but interrupted by his brother. Meanwhile, Alex leads an operation to expose the Collaborators' plans to sink the President's reputation, and teaches Owen to trust his instincts.
For three years, Alex has a peaceful, anonymous life in Italy. However, Alex must abandon this idyllic existence when Ryan persuades her to help him rescue Shelby from an international arms dealer, The Widow.
When a physics professor at a major U.S. university steals weaponized uranium, the team scrambles to find the professor and the missing uranium before it can be used against an important international summit meeting in New York City.
The team must protect a scientist who has developed a deadly technology that, in the wrong hands, could have devastating consequences to mankind; Ryan and Shelby stumble on something of Alex's that signals a possible change in her personal life.