The idea that someone in the FBI decides to frame Alex as a domestic terrorist. But the scary fact is that it took a long time to plan after Alex was qualified to enter the academy.
Alex's world comes crashing down after her FBI colleagues don't believe that she's not a terrorist.
Alex is forced to take down a fellow FBI agent and a civilian because they assume she was the terrorist responsible for bombing Grand Central Station.
The training simulation done in Quantico.
Simon figures out that Langdon manipulated a crime scene to tie it to a serial killer, and she gets this close to murdering him.
Shelby realizing that the "half-sister" she's been supporting with millions of dollars over the years as a way of connecting to her only family is a con artist bilking her this entire time.
Natalie being captured by the Big Bad and rigged up with a suicide vest set to detonate if she and Alex don't do as the Big Bad says.
A group of CIA agents going rogue in conducting a terrorist attack.
Owen challenges the recruits to use all the enhanced interrogation methods he taught them, on him. It truly crosses over into nightmare territory when Dayana, who apparently has past experience, tells them to use Lydia as a target to get him to give up his information.
Dayana is tortured in front of Alex.
Terrorist:[holding hammer over Dayana's spine] Here, no walking.
Dayana's sister was probably raped in front of her.
Fear and Flesh
A weaponized TB attack on ten cities in the USA was nearly successfully initiated. As it is almost fifty people died of a "test run" attack.
In addition, Ryan having to beat Owen Hall as part of a staged incident to give him credibility with a white supremacist movement leader.
The Heavens Fall
Jocelyn is kidnapped and forced to engage in mortal combat with a bag over her head and heavy gloves on her hands, which, combined with her hearing impairment, effectively robs her of all of her senses. Her opponent very nearly kills her. And then, after she kills her unseen opponent, she finally gets the bag off of her head, and discovers that her opponent was Celine.
The Art of War
One minute, Jocelyn is going to retrieve something out of the refrigerator. The next minute, the loft is being stormed, Owen is shot, and the intruders come this close to killing Jocelyn, who is completely unaware of the danger because it's going on behind her. For added effect, there is no sound during this scene.