Annie resigns from the CIA and asks Ryan McQuaid for a job. He hires her with the understanding that a personal relationship is on track. She uses her position to infiltrate his computer system for information about the dog walker.
Auggie breaks an encrypted file and finds information about a project called "Flint." Annie tries to get Arthur's help to get more information on the dog walker now that they know his name, but he wants to be looped in first. She decides to not get his help.
Ryan feels guilty about lying to Annie and he tells her about Flint and that it's a black op group doing missions for the government. She's not sure if he's telling the truth or not. Auggie suggests that Ryan knew she was on to him and told her to gain her trust.
Annie goes to Arthur with the information and he comes back with an address for her. She checks it out and Caitlyn follows her. They find the dog walker and other Flint team member at the facility. They attack the women and Caitlyn kills one of them. The dog walker escaped. The facility looks like it was used to plan a mission.
Annie, Catilyn and Arthur review the site and determine it was used to practice the Chicago bombing. They take samples and bring the information to the CIA. They confirm the same explosive was used. Ryan McQuaid is named a suspect and being pursued.
Ryan shows up at Annie's place because he was tipped off that he's under investigation. He wants her help, but she pulls a gun on him. He convinces her that he's being set up or at least convinces her enough that she lets him leave. When Auggie asks her if Ryan would go to her, she says no. She lies.
Calder investigates Annie's altered medical records for the DCI. When Auggie won't come clean, Calder takes his operatives away. Joan convinces Calder that everyone has secrets (he does!) and he puts Auggie on the Chicago investigation.