While at an aquarium during birthday, Arion's birthday, Neil was seen working on a code while talking to his wife, Elsa. The two began to argue because Neil was spending more time working and less time with his son. After the argument, the two were shocked to see that Aaron had gone missing and was nowhere to be found. Elsa went off into a section of the aquarium while Neil went another way, encountering Julian in the process. Julian said he'd be able to help Neil find his son...and his wife (A Free Agent).
After getting captured, Neil was taken to a warehouse and was ordered by Sloane to help him build a Rambaldi artifact. Even though Neil felt like he had been captured, Arvin assured Neil that he was actually helping himself.
Neil didn't want to help Arvin until his family was released, but Arvin changed his mind when he heard his wife's pleas. Neil told Arvin that it wasn't possible to build the artifacts unless he had magnetometer. Arvin told Neil it was in the vault of Amcore Bank and he leaves Neil to go steal the magnetometer.
When Sydney pays a visit to the recently captured Elsa Caplan (who is discovered to be working for the Russians), she discovers that Neil has been implanted with a suicide pill underneath his skin. Sydney wants to rescue Neil, but Jack is resistant to the idea. She devises a plan to rescue him herself (Endgame).
When Neil becomes fed up with Irina's complaints, he tries to strangle her to death; Sloane shoots him in the leg. He puts the gun to Neil's head, but he tells Sloane he doesn't care if he dies anymore. Irina manages to take Sloane away and saves Neil, stating they still need him. Neil asks Sark why a someone like him is working for Sloane, to which Sark tells him he's working to acquire something he never had.
Sydney is able to track down his location, with the help of Vaughn. As Vaughn chases after Sark, Sydney finds Neil. She informs him that a cyanide pill is about to kill him and that his wife is working for the Russians. He already knows, and says he's working for the NSA. After learning that his wife implanted the capsule, Sydney cuts out the pill. When they are reunited, Neil and his wife say they still love each other - and kiss each other shortly after Elsa is released.
Neil had put an algorithm in place that, once decrypted, allowed them to locate Sloane and Irina.