The 12th episode of CIA begins with a flashback to a year ago in Mindanao, Philippines, where Toni and Colin are having sex. Colin notices the dove tattoo on Toni's back, which she explains is a symbol of her childhood memories of her dad's love for doves, despite their humble upbringing.
Later, she leaves to run SDR, concerned that their mission might be compromised. She asks Colin to meet her at a restaurant later. She goes off to meet a Filipino man working at NIC who informs her about a co-worker who leaked classified intelligence and caused the deaths of several people. The man is worried that Pyramid will come for him because he has linked them to the leaked intelligence. Toni assures him that she will do her best to protect him.
However, a man named Harry arrives at the bar, warning that Toni's identity as a double agent is about to be discovered. Apparently, Joanne, the boss, wants Toni to go off the grid. They take Toni with them and blow up the place. Toni is injured, fearing that Colin, who is running late, might have been caught in the blast.
News of Toni's survival shakes Colin to his core, and he starts to question everything she has ever told him. Bill brings him to the FBI office to give an update on the case. With Kevin Turner identified as the CIA mole, the FBI is relieved that Bill completed the mission. They are unsure about Pyramid, but Colin and Bill promise that they are looking into it.
They ask who took out Kevin, and Colin gets defensive, refusing to tell them about Toni. He insists that the CIA will take the fallout and handle the rest of the case. In the meantime, Nikki's superior asks her to bring Toni in alive. This proves to be difficult given that Harry has put out a hit on her. After taking down one of Harry's assassins, they use his phone to set a meeting with Harry.
At the meeting, Toni tries to take out Harry but fails, and the team rushes him to the hospital. During the encounter, Colin gets a chance to talk to Toni, but she refuses to tell him what is really going on. She only says that she needs to finish the mission and that everything she did had nothing to do with him. After she escapes, Colin stops hiding her identity and officially identifies her as the shooter.
Later, they question Harry, who claims that Toni had always been dirty and that she left Colin for dead in the Philippines. Colin threatens to kill him if he doesn't tell them who ordered the hit on Turner. Harry claims that Toni went rogue and has been killing Pyramid's assets. He plays them a message Toni sent, vowing to kill them all. Harry asks for immunity and protection in exchange for what he knows.
The truth behind Pyramid's seemingly innocuous surface is far from straightforward. CEO Joanne, blissfully unaware of the dark underbelly of her company, believes that a merger with new investors will elevate Pyramid to new heights. Unbeknownst to her, this celebration is actually a hostile takeover orchestrated by one of her own subordinates, Harry, who has turned Project Bingham—a spy program—into a global network of corrupt agents selling intelligence to the highest bidder.
When Bill receives a call from Toni, alerting him that someone has broken into his house, Colin checks his place and discovers the bug Toni had hidden there. He leaves her a message, starting with a question about her betrayal and ending with a threatening one.
The party takes a shocking turn when Toni reveals her true intentions—not to harm Joanne but to save her from Harry's ruthless men. In the midst of this chaos, Harry escapes from the hospital and arrives at the party, only to be killed by Toni in an effort to save Joanne and Bill. She explains that her real motive was to dismantle Project Bingham from within.
While Colin is hurt and distrustful, Bill finds her explanation plausible. They realize they are running out of time as the hostile takeover begins in earnest. Colin rushes back to the party to save Sara but ends up being shot. Despite this, they all manage to escape alive, including Joanne.
Jubal offers Bill a promotion, but he declines it to remain by Colin's side and continue as his partner. The CIA decides to send Toni back into the field to track down the remaining rogue agents of Project Bingham. The season ends with a sense of uncertainty and anticipation for what lies ahead.
