Episode 1 of The Night Agent Season 3 begins with a flashback to a young Peter playing with his toys while his mother is on the phone with her doctor. She receives distressing news but hides her sadness and later urges Peter to always do the right thing, even when it's difficult.
In the present, we reunite with Peter in Juan Dolio, Dominican Republic. He's there on an undercover mission to arrest a married couple selling stolen military blueprints from the Pentagon. He successfully concludes the mission.
After wrapping up the Dominican Republic mission, he returns to the US and meets with Mosley. It turns out that President Hagan has been deploying more night-action agents, and the institution is feeling a bit strained. Peter and Mosley worry that Hagan might be compromised, and his move to deploy new night action agents might be an attempt to hide his compromising ties to Monroe, the broker.
Even though Peter has closed four cases in six months, he doesn't want to go back to New York. He wants to stay away to protect Rose. Peter has been working himself to the bone because he's anxious, waiting for Monroe to call. He also feels guilty for his role in how Hagan came to be president. He convinces Mosley to give him a new case.
Mosley tells him about the recent death of Benjamin Wallace, a supervisor at FinCEN (the Financial Crimes Enforcement Network). They believe he was killed by one of his junior employees, Jay Batra, who then fled to Istanbul after stealing classified documents. Meanwhile, a commercial flight (Flight Pima 12) is brought down by a missile, killing all passengers on board.
Hours later, Peter finds himself in Istanbul, Türkiye, following the semi-cold trail Jay left. He gets word from a restaurant owner and waiter that Jay was seen at the establishment a few minutes back. While there, he notices a news report of Hagan offering his condolences and warning that he won't tolerate terrorism.
After getting Jay's outfit description and his next destination, he quickly leaves. Thankfully, he spots a nervous Jay and trails him. He watches as Jay leaves an envelope at one of the train lockers at the Sirkeci Train Station. Unfortunately, Peter is distracted by a woman in a queue and loses Jay. He later notices a group of men chasing a train that they believe Jay got on.
Peter stepped back inside and waited to see who would pick up the envelope Jay had left in the train lockers. Soon, a woman arrived and he followed her to a nearby pub. There, he struck up a conversation with her, flirted with her, and surreptitiously glanced at her details on the receipt. This led him to her hotel room, where he discovered a ticket to a soccer match at Beşiktaş Stadium. Meanwhile, he received a call from Catherine, who warned him to be careful after his debriefing with her. It turned out that the woman at the pub was Isabel, a financial reporter for The Financial Register. Catherine and Peter found it strange that Jay was passing off information to a journalist when he should have been keeping a low profile. They questioned whether he had killed his boss, considering his previous reputation as an upstanding citizen until the fateful night his boss was found dead in his apartment.
As expected, Peter followed Isabel to the soccer match and noticed the men from the train station were there too. Once Isabel met with Jay and left, Peter made his move. He approached Jay and warned him about the men tailing him. He promised to safely get him out as long as Jay promised to give him the original classified documents he had left at his house. Peter handed him his cap and disposed of his phone. With the cheering crowd going wild, the two made their way out. Unfortunately, on their way out, they ran into Isabel, who recognized Peter and pushed him away, trying to give Jay enough time to escape. Jay made a run for it, but as he emerged outside the stadium, he was captured by one of the assassins. The assassin brought him to the car and radioed the others. Peter arrived before them and overpowered him. He then got inside the car, and they sped off. The other assassins gave chase on motorbikes.
A wild car-motorcycle chase ensues, with bullets flying all around. Despite the chaos and a lot of improvisation, the team finally manages to lose the assassins. Later, Peter calls for a night action and asks for an extraction. Unfortunately, with the institution stretched thin, they are asked to wait until the following morning. Peter decides to book a place to spend the night. As they walk there, Jay tells Peter that he didn't mean to kill his boss. Apparently, Jay had flagged numerous Suspicious Activity Reports (SARs) involving large crypto transfers from American companies to an offshore wallet. He brought this to Wallace's attention, who asked him to drop it. A few days later, Wallace shows up at Jay's house, grilling him about the documents. Suddenly, Wallace draws his gun and apologizes, saying someone ordered him to kill Jay. A fight ensues, and the gun goes off. In a panic, Jay flees the country and takes his hidden copies of the classified documents with him since Wallace destroyed everything else. Jay also mentions that his cousin helped him settle in Istanbul and asks Peter to call and warn her that she is in trouble. Peter tells him they can't as it will reveal their location. He offers to call someone from his team to reach out to Jay's cousin. Peter suggests lying low until they get a chance to retrieve the copies of classified documents. Jay had initially claimed he left in his hideout. This is when Jay reveals he had no other copies apart from the one he gave Isabel. Finally, they get to the house, and Peter makes a call to Catherine and briefs her about Jay and Isabel having the documents. Catherine agrees to at least give Jay the benefit of the doubt as they try to find evidence that corroborates his story.
Jay takes this opportunity to use the landline to call his cousin. As time passes, Jay confesses that he is afraid there might be no evidence to back his story up. Peter assures him that he has been there, and they will look into how to help him. Suddenly, the assassins pull up at their location. It turns out they traced them through Jay's phone call to his cousin. Peter and Jay flee and hide in what looks like an abandoned building. Peter takes on the assassins while Jay finds the exit. After successfully overpowering and killing the assassins, Peter convinces Jay to trust him. In the end, Jay opts to stay with Peter and return to the US.
The next morning, a helicopter arrives to extract Peter and Jay. Before boarding, Jay reveals that some of the classified documents hint that the Prima 12 terrorist attack wasn't random and that some American companies might have financed it. He believes the terrorist attack was allowed to happen for either a political or financial purpose. Just then, Peter receives a call from Monroe on his burner phone. Surprisingly, Monroe wants Peter to deliver Jay to him.
