In the opening of Episode 1 of The Night Manager season 2, a flashback takes us four years after Roper's arrest in Egypt. We're reunited with Jonathan and Angela in Syria, where they're there to identify Roper's body. According to Angela, no one, even Danny, will ever find out that Roper is dead. Angela is forced to identify the body by herself and confirms that it is indeed Roper.
Two years later, we meet Jonathan in London, working under Rex in the new Night Owl Unit. This time, he's going by the name Alex Goodwin. Even after six years, his memories of Roper continue to haunt him. Nevertheless, he lies to his work-mandated therapist that he's doing well. This causes her to grow increasingly concerned that Jonathan will explode one day.
Professionally, Rex and Jonathan are doing well. Marya, the new Riverhouse Supervisory Council chair, extends the Night Owl Unit's contract for another three years. One random night, the team comes across Jaco while watching a man linked to the Bulgarian mafia. Jonathan quickly recognizes Jaco as one of the soldiers who worked at Roper's military haven.
The following morning, Jonathan gatecrashes Rex's birthday party to tell him about Jaco. He overhears and sees Rex talking to a certain woman. The woman quickly leaves, and Rex asks Jonathan to forget what he saw. When Jonathan brings up Jaco, Rex asks him to drop the matter and focus on the task at hand. He insists that there's no need to awaken the dead and ruin Jonathan's new identity. Before Jonathan leaves, Rex gives him his new number. Jonathan opts to stay for the party and runs into Marya.
In the evening, Jonathan asks his team to trust him and continue surveilling Jaco. The team follows Jaco and listens in on his new deal with a British man. They realize that Jaco is working with a mysterious man who considers himself Roper's true disciple.
A deeper look into the man Jaco met leads them to Marya's house. Worried, Jonathan calls Rex. The latter asks Jonathan to secretly meet him at his house. Unfortunately, the next day Jonathan receives a call from Rex's wife informing him that Rex has died. Since he's already on his way, Jonathan gets to Rex's house quickly. Basil informs him that Rex supposedly took his life.
After the police leave, Celia informs Jonathan that Rex was agitated and wanted to speak with him about Jaco. Jonathan swiftly searches Rex's office and discovers his burner phone. Within, he finds a link and upon checking, he discovers more evidence of Marya's involvement in some shady business. He also finds more information on Teddy, the supposed true Roper disciple. As he goes through the files, Roxana calls Rex's burner phone. Jonathan orders his team to trace her but insists that they switch from watching from the sidelines to being field operatives. He also mentions how Riverhouse is compromised and might be involved in Rex's death. He promises to tell them everything once they complete the mission.
Jonathan then interrupts Roxana's dinner and brings her to a motel. There, he questions her about her relationship with Rex. She reveals that she was Rex's asset and was investigating suspicious shipments at her shipping company. Roxana denies knowing anything else or ever meeting Teddy. Jonathan leaves her in the care of another agent, Tony.
Meanwhile, another agent at the office investigates the latest shipment made by Roxana's company. They quickly discover that there is an incoming ship linked to Teddy's company, Barquero. Aside from being a businessman, Teddy is also running a charity foundation called Aurora. This reminds Jonathan of Roper's haven project. He asks Sally to find a way to stop the ship from reaching the Cartagena port.
Meanwhile, Jonathan returns to review the Roper files and later visits Danny at his school. Unfortunately, Danny is not pleased to see him and refuses to cooperate. He blames Jonathan for what happened to his family and becomes even more agitated when he learns that his father died six years ago and no one bothered to tell him.
At the motel, Roxana outsmarts Tony, steals her phone back, and sends a message to someone. Simultaneously, Jonathan gets his team to travel with him to Colombia to follow Jaco and see who he meets. They manage to put a tracker on the diplomatic bag that Jaco is carrying.
Jonathan and his team follow Jaco to a hotel in Colombia, where he meets with Teddy. However, Teddy confronts Jaco before they head to their assigned room, where Jonathan's team is waiting. He kills Jaco and two members of Jonathan's team. In London, someone kills Tony and takes Roxana with him.
Back in Colombia, Teddy calls Jonathan to ask who he is. At the time, Jonathan is rushing to get to the hotel room Teddy had initially booked. He breaks the hotel room door and discovers a bomb wrapped around Jaco's body. He starts running just before it explodes. The episode ends with Teddy nonchalantly walking to his car as chaos erupts behind him.
