On Quantico Season 2 Episode 12, Alex and Owen search through Lydia's emails to try to uncover more about the AIC. In addition to the names of the current recruits, Owen discovers something that the AIC wants, and he creates a lesson at the Farm designed to help the AIC get it.
Sure enough, Lydia comes into town to help lend a hand at the Farm, while instructing her AIC recruits to perform their own side mission. What does the AIC want? Access to the NSA, of course. During the mission, Alex and Harry discover that the AIC tapped the NSA, and Dayana makes sure Leon is made, and thus forced to leave the Farm.
In the present, Alex and company lead the hostages through a tunnel to safety, but there's a hidden agenda. Will outs himself as being capable of figuring out who is AIC, thus making every AIC member want to take him out. He's the bait, and the trip in the tunnels is a stalling tactic, giving the AIC time to act.
Don't worry, the AIC doesn't waste the opportunity. Carly puts a gun to Harry's head, saying to hand over Will or Harry dies. Yup, Carly is AIC. Sebastian has to choose between his wife or the man he probably loves, and he picks Harry. Carly shoots him first though. Sebastian is still alive, but Carly is not.
Everyone makes it out of the tunnel, except for Dayana and Will. When Alex goes to the FBI for help, she finds Lydia, who is asking her for help.