On Quantico Season 2 Episode 8, Alex calls Shelby, who notifies her that the FBI has identified a biological weapon on the roof at the terrorists' main base of operation. Alex and her ragtag former Farm mates set out to destroy it. When Alex and Sebastian come to the biological weapon, they discover that it isn't actually a weapon - it's a self destruct mechanism.
The weapon will only gas those inside the building, and no harm will come to the world outside. As Alex regroups with the rest of her friends to figure out a game plan, Leon and Diana break the bad news that the bunker is being destroyed. Then, they are surrounded by terrorists, and they are being separated.
Alex fights back against one of the terrorists, knocking off his helmet. It's Ryan. He pushes Alex out of the way, and he shows that she is now outside the perimeter. If she tries to get back in, the weapon goes off.
Back at the Farm, the AIC makes Ryan kidnap an old man and bring him to a warehouse. Unbeknownst to him, once he leaves the man, Leon comes to kill him. Then, Leon leaves, and Diana cleans up the mess.
All three of them are told to return to the warehouse, and now they see that they've all been tapped. Then, their phones go off with surveillance footage of them doing whatever they were tasked with doing, and the AIC lets them know, A style, that they're in because now the AIC can trust them. Blackmail is a great thing, is it not?
Alex learns that she has been kicked off the mission, and Miranda can get her back in active duty in New York in 5 months. Alex turns her down, and she says that she is going to stay at the Farm and track down the AIC.