Arthur resigns, saying he had an extramarital affair. He asks Annie to find out if Henry knows Teo is his son. Annie and Auggie continue their investigation and find a mole in the CIA. They learn Arthur never cheated but lied to protect Joan.
Annie meets Arthur and tells him there is a bomb threat against Teo. Arthur tells Annie that Teo is a double agent. Annie goes to Columbia to determine Teo's allegiance. Joan is asked about her qualifications for head position at the agency.
Annie follows two Chinese nationalists working in Washington DC as they are involved in the funding a terrorist bomb attack. Joan is now the head of clandestine affairs; Auggie is promoted to interim head of DPD. Henry vows to kill Teo.
Calder Michaels replaces Auggie as interim DPD head. Auggie learns Calder is the new mole for Henry. Calder traced money from the Chen's to a terrorist in Vienna; she is sent there to gather information. Joan and Arthur get back together.
Seth Newman's body is found. The FBI is investigating his death. Annie manages to be part of the FBI team so she can prevent them from finding out her involvement. Henry knows Annie is involved but still makes her an offer to join his team.
Auggie finds out his former partner, whom he loved and saw shot, is still alive. Annie works with her to locate missing weapons that Henry might be selling to terrorists. Calder learns Annie is lying about events from a previous mission.
Annie tracks down Teo to ask him to question Eduardo about Henry's involvement in stolen weapons and bombings. Eduardo is killed by Henry's men. Calder confronts Joan about evidence Annie has hidden. Calder goes after Auggie for evidence.
Calder interrogates Auggie, and Auggie realizes Calder is not working with Henry. Teo goes after Henry but Annie aborts his shot. Henry captures them and frames Teo for missile fired at a plane. Annie and Teo escape, but Teo is badly shot.
Annie is in Germany to get proof against Henry. Calder arrives Germany to track Annie. Senator Pierson wants Joan out of office. Joan has pregnancy problems and goes to the hospital. Annie and Calder meet to talk. Annie is shot and goes off grid.
Henry reaches out to his only ally within Langley - Calder. Joan reveals something during her deposition that puts a wedge between herself and Arthur. An old flame reveals she still holds a torch for Auggie.