After clearing her name, saving millions of lives, and discovering the mastermind behind it all was the very man who had trained her at Quantico, American hero Alex Parrish was given a shocking reward: she was fired by the FBI. But now she has been given the chance to serve her country again: in the clandestine ranks of United States' top intelligence agency, the CIA.
A diverse group of recruits has arrived at the FBI Quantico Base for training. They are the best and the brightest so it seems impossible that one of them is suspected of masterminding the biggest attack on New York City since 9/11.
Alex is on the run and must outsmart Liam and his team to get into her apartment for anything that could help clear her name. Meanwhile, in a flashback to Quantico training, the NATS are tasked with finding a needle in a haystack while looking for potential threats to national security.
At Quantico, Alex finally receives information about her father and his FBI past, but in the future it’s her mother, Sita, who plays a key role when Liam convinces her to participate in a press conference on national television begging Alex to turn herself in. Also at “Quantico,” the NATS learn the art of profiling and focus on their classmates’ strengths and weaknesses, ultimately challenging their confidence and comradery.
At Quantico, the recruits are tasked with performing a hostage rescue training exercise that shakes Alex, making her question her ability and whether she should quit Quantico. While in the future, Alex continues to search for clues, finding one that questions the innocence of one of her closest classmates. But is her clue really what she thinks? No one is who they seem.
The trainees leave campus for the first time while undergoing their first undercover assignment. With an evening full of unpredictable events, Alex and Ryan find themselves getting close while the recruits’ skills are tested. In the future, Alex decides to tell her side of the story and sits down for her first public interview leaving everyone watching to wonder who is really telling the truth.
The NATs learn surveillance by putting it into practice with Miranda and her troubled son, Charlie. Shelby tries to keep Caleb at a distance, but Raina opens the door to a closer relationship with Simon. In the future, Alex is helped when she tries to hack into an FBI computer.
It’s midterm exam time at Quantico where the NATS are given an explosive assignment which results in some people going home for good. In the future, Alex continues to try and clear her name, finding Nimah and Raina who provide more questions than answers leaving Alex and the world to wonder, “who can you really trust?”
In the future, the FBI computer system is hacked and confidential files go public leading Alex to the conclusion that a second bomb is in play somewhere in NYC. Back at Quantico, the recruits are given individual assignments only to realize they are all connected as part of a lesson to look at the bigger picture.
At “Quantico,” the NATS attend a class with guest speaker Dr. Susan Langdon, played by Anne Heche. Dr. Langdon is a former agent and profiler who tasks the trainees with looking at serial killer cases to find the one victim that doesn’t fit the case, but when Simon becomes too good at finding things that don’t belong, it’s his life that becomes endangered. In the future, Alex is interrogated by a highly sophisticated FBI team while Ryan’s life hangs in the balance.
At Quantico, an emergency disciplinary hearing causes deep secrets to be spilled, while in the future Alex works covertly with her team to find the real bomber before her time runs out.
The terrorists responsible for the bombing of Grand Central Station finally reveal themselves, but instead of answers, more questions remain. While back at Quantico, the recruits receive a well-deserved few days off for the holidays, but not everyone is oh so merry when secrets are revealed and lines and blurred.
Alex finds herself in the middle of a congressional hearing to testify about the terrorist bombings. Convinced Elias didn’t act alone, she is determined to find answers and the truth. While back at Quantico, a new group of NATS join Alex and her classmates, causing tension and competition between the groups of trainees.
This week the NATS learn how to source information from confidential informants, but when they test their skills in the real world, they soon realize being an agent is not as easy as it seems. Meanwhile, in the future, Alex and a fellow agent find themselves in a life or death situation when they are forced to provide classified information that could result in deadly consequences.
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. Even though his friends try and help him, it’s uncertain he will ever be the same again.
A terror cell tries to infiltrate Quantico, forcing Miranda and Liam to pay a deadly price. While in the future, Alex continues to get instructions from the terrorist – only this time, it’s Claire Haas’ (played by Marcia Cross) life that hangs in the balance.
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 and stop the terrorist from striking again.
At Quantico, the NATS’ 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, the NATs look into each other’s background to determine who gets high-level security clearance, and in the process Alex, Shelby and Iris learn some surprising truths about Drew, Will and Caleb. Meanwhile, in the future, Alex contacts Claire Haas (guest star Marcia Cross) in order to find her missing friends and is shocked when she discovers what happened to Cale.
It’s career day at Quantico as the NATS meet representatives from various FBI branches to help them decide their future paths. In the future, Alex continues to search for the terrorist, and in the process, discovers some familiar faces – including one who knows the terrorist’s endgame.
With only a few weeks until graduation, the NATS are dispatched to various field offices where Alex and Ryan find themselves working a case together. Meanwhile, in the future, Shelby and Caleb's relationship takes a turn, and Alex doesn't know who to trust when she discovers new information about the man she loves.
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.
It’s graduation day for the NATS of Quantico, while, in the future, Alex and her team find themselves head-to-head with the terrorist.