"We believe that some people in the agency decided that they are done with these laws. They want the old ways restored - no accountability, no rules, no oversight. Whoever this rogue group is, they have been growing within the CIA for years with their own nefarious agenda, and we need to stop them."
Along with the help of Miranda Shaw and the FBI, he leads the joint undercover operation to respond to growing domestic threats within the CIA. He and Miranda had Alex Parrish and Ryan Booth infiltrate The Farm as part of an operation to investigate a rogue intelligence faction of the CIA called the AIC.
In GLOBALREACH, it was revealed that he resigned from his position at the Agency.
He was forced to resign, as a result of blackmailing tactics initiated by Alex and Alice Winter. They highlighted, that if Keyes disagreed to resign, they would expose him as being part of the task force, which would negatively affect the reputation of the Agency.
In RAINBOW, he understood Alex's position as she was forced to complete the tasks assigned to her by Alice as Alex needed to gain their trust, as part of her undercover mission, to expose the secrets of The Collaborators.