The opening scene of CIA unfolds with a man, armed with an energy weapon, pointing it at an office building across the street. The workers inside start to experience seizures, prompting this man to walk over and make a drive copy of something from one of the computers. The scene then cuts to Colin dropping off a woman at her place when he receives a work call. He quickly excuses himself and calls back. Shortly after, he arrives at the scene and spots the FBI at work. He calls someone and promises to find out as much as he can.
In the meantime, Jubal and Special Agent Bill are interviewing the office manager. It turns out that the company has contracts with the government to manufacture weapons. Colin sneaks in and lies, claiming he is from the DOD, when Bill spots him. However, Bill finds it weird and asks Jubal about it. By the time he turns around, Colin is already on his way out. Bill tries to chase after him but loses him.
Colin meets with Nikki and informs her that he thinks his CIA asset, whom he rescued from Venezuela and got a job at the company, is behind the attack. However, he has no idea whether Adrian has turned or if something else is up. He asks Nikki to find him a good FBI liaison to work the case with. As it turns out, Jubal has just the person for Nikki's team. He recommends Bill, who by all means is a rule follower and not one to be messed around with.
When Jubal brings up the new FBI-CIA fusion cell, Bill immediately asks why he was picked. Jubal informs him that it's because he knows how to toe the fine line. A few hours later, Bill makes his way to the secret CIA office in New York and comes face-to-face with Colin again.
They instantly develop a mutual dislike for each other. Colin is offended by Bill's belief that Adrian is a double-dealing asset who played him for a fool. He also doubts Bill's ability to navigate the grey areas of their work. Bill, on the other hand, dislikes Colin's methods of handling situations. Nikki attempts to mediate and convince Colin to work with Bill, but he stubbornly refuses.
After a brief briefing, Colin excuses himself to follow a lead. Although he asks Bill to stay behind, the latter secretly follows him after calling Ian for assistance in tracking down a man whose name was mentioned in connection with Adrian. It turns out that the man, Bobby, is Adrian's boyfriend. Bobby calls Colin after spotting a suspicious man following him.
At the same time, Bill takes action and tries to arrest Bobby as he tries to slip away. The man who was following Bobby starts shooting and hits Bill in the shoulder. They rush Bobby to a secret doctor who normally works for the CIA. While the doctor tends to Bobby, Colin confronts Bill for following him. Meanwhile, Nikki convinces the senator to reveal more about the capabilities of the stolen software.
Back at the makeshift secret hospital, Bobby reveals that Adrian has stopped taking his medication and is experiencing hallucinations. He believes that Adrian has been talking to the wrong people on his phone and taking pictures of their conversations, all of which were encrypted. The last time he spoke with Adrian, the latter asked him to prepare to leave the city and meet at JFK later that night. Obviously, they begin to worry that Adrian has turned and may try to flee the country before or after selling the weapon software.
Despite the bleak circumstances, Colin resolutely refuses to abandon Adrian. Elsewhere, Gina decrypts the messages and discovers that Adrian is meeting someone at the park in 90 minutes. The CIA team hastily prepares for a sting operation. Unfortunately, one of the men starts shooting, causing chaos and loss of sight of the individual Adrian was supposed to meet. Thankfully, they were able to tag and identify him as a low-level Venezuelan arms dealer named Jorge Santos. Colin follows the trail but finds Jorge dead, with the USB drive containing the software missing.
After the botched operation, Colin and Bill engage in a heated exchange. Colin demands that Bill aligns with his methods or return to the FBI. They wait for Adrian's medication to take effect before interrogating him. It emerges that Adrian was displeased with how his employees were attempting to weaponize something he had created. He thought he was speaking to a journalist's assistant but was actually about to hand over the information to a notorious arms dealer known as Saul, who often posed as a journalist to gain access to his targets. After assuring Adrian that Bobby is safe, Colin leaves him with Bill while he goes to meet another asset.
Meanwhile, Adrian confides in Bill about how Colin risked his life and career to save him and Bobby from a Venezuelan mafia boss. In the meantime, Colin meets with an asset named Sonya who reveals that Saul is planning a demonstration later that evening. He has asked his clients to watch the skies over the East River at 4 pm. Colin and Bill convince Nikki to launch a helicopter over the East River to buy them time to locate the weapon and have Adrian take control. Bill also enlists the help of his pilot friend Charlie to fly the helicopter. Thanks to their efforts, they are able to find the weapon, arrest the arms dealer, and prevent Charlie from an untimely demise.
After the operation, Bill and Colin reunite Bobby and Adrian. As they walk home, Bill admits that he was too quick to judge Colin. He also reveals that he doesn't trust anyone due to past experiences. He teases Colin about lying about reading his file and jokes about the possibility of becoming friends. Bill returns to the FBI and briefs Jubal, calling Colin a liar but claiming he can handle him. Jubal informs him that he has been permanently assigned to the CIA-FBI fusion task force, apparently with the aim of finding the mole in the CIA's New York operation.
