V úvodním dílu se seznámíme s různorodou skupinkou nováčků FBI, kteří začínají svůj trénink v Quanticu. Patří mezi ty nejlepší a proto se zdá neuvěřitelné, že by jeden z nich stál za ničivým teroristickým útokem.

Alex musí na útěku přechytračit Liama a tým agentů, aby se dostala do jeho bytu, kde by našla něco, co by očistilo její jméno. Ve flashbacku sledujeme nováčky v Quanticu při úkolu, jehož cílem je zjistit případné teroristické hrozby.

Alex se konečně dozvídá více o svém otci a jeho minulosti v FBI. V současnosti je to však její matka, kdo sehraje důležitou úlohu poté, co ji Liam přesvědčí, že během televizního vysílání požádá Alex, aby se vzdala. Ve flashbacích pak sledujeme nováčky, kteří se zdokonalují v profilování a snaží se odhalit slabé i silné stránky svých kolegů.

Nováčci procházejí tréninkem na záchranu rukojmích a Alex poprvé pochybuje o tom, zda je schopná práce pro FBI a měla by zůstat v Quanticu. V přítomnosti pak pokračuje v hledání důkazů, že jeden z jejích kolegů stojí za teroristickým útokem. Vodítko, které najde, by mohlo ukazovat na viníka, ale nic není takové, jaké se zdá.

Nováčci poprvé opouštějí areál akademie v Quanticu během své práce v utajení. Večer plný událostí otestuje jejich schopnosti, zatímco se někteří z nich sbližují, především Alex s Ryanem. V přítomnosti se Alex poprvé rozhodne před veřejností promluvit o svém případu. Uvěří jí ale někdo?

Nováčci se učí sledovacím technikám, které si cvičí na Mirandině problémovém synovi Charliem. Shelby si snaží držet odstup od Caleba, zatímco Raina se více sbližuje se Simonem. V současnosti se pak Alex snaží napíchnout na servery FBI.

V Quanticu se všichni připravují na první zkoušky a nováčci dostanou úkol, po němž někteří z nich budou muset akademii opustit. V současnosti Alex vyhledá Nímu a Rainu, ale místo odpovědí se vyrojí další otázky ohledně toho, komu může skutečně věřit.

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. 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’ 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.