Alex está na corrida e deve ser mais esperta que Liam e sua equipe para entrar em seu apartamento para qualquer coisa que poderia ajudar a limpar o seu nome. Enquanto isso, em um flashback de formação Quantico, as NATS (analistas) têm a tarefa de encontrar uma agulha num palheiro, enquanto à procuram potenciais ameaças à segurança nacional.

Em Quantico, Alex finalmente recebe informações sobre seu pai e seu passado no FBI, mas no futuro é sua mãe, Sita, que desempenha um papel fundamental quando Liam a convencr a participar de uma conferência de imprensa na televisão nacional implorando para Alex se entregar. Também em "Quantico," os NATS aprendem a arte de criação de perfil e se concentrar em pontos fortes e fracos de seus colegas, em última análise, desafiando a sua confiança e camaradagem.

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. 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.