On Quantico Season 2 Episode 13, Lydia, Alex, Harry, Leon, and Ryan go back into the crisis zone to try to find Dayana and Will. Lydia says Dayana stayed behind for the AIC mission, uploading the drives.
When Alex finds Dayana and Will, they claim that they are destroying the drives. Lydia is Dayana's boss, and Dayana was instructed to hide out in the crisis center with the drives and Will. Guess what? Lydia is AIC!
Lydia manages to upload one drive. She says it will help weed out corruption in the government.
Two weeks later, Alex, Dayana, Ryan, Nimah, and Shelby are summoned by President Haas and Matthew Keyes. It turns out the drive that was uploaded had America's reaction plan to any attack, so in the wrong hands, someone could attack America without the country even knowing.
They have been assembled to hunt down the AIC and figure out who is going to attack the country. The team will report direct to, wait for it, President Haas' son. Caleb is alive!
At the Farm, Sebastian exposes Harry's NSA hacking to Matthew Keyes, which gets him kicked out of the Farm aka exactly what Harry wanted. In return, Harry tells the group that's he is MI6.
The explosion that Alex and Harry witnessed killed Jeremy Miller, the former recruit who was kicked out. The FBI thinks Owen was behind it, and Owen takes a plea deal and goes to jail. As soon as the cuffs are put on him, Lydia tells Alex to pack her bags.