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, 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 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.

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, 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.

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.

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.

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 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.

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.

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.