Sammy, a Pakistani and undercover anti terrorist agent for the US, is shot after a cricket match in Central Park. Frank, Soren (the head of intelligence) and Danny are the only ones who know Sammy is a cop. Danny is assigned to the case and must keep this information from Jackie, who is perplexed by the priority of this case. Sammy's cover cannot be blown as 2 years of work has gone into infiltrating a terrorist cell, and an attack is expected in 48 hours that other undercovers must stay on top of to prevent.
Danny and Jackie investigate internet threats made on Sammy's life and are lead to an Islamic shop, and meet Malik, an employee. They find a motorcycle helmet and motorcycle identical to the one used by the shooter confirmed by license plate, on camera around time of shooting; and later find the gun in his apartment. Malik admits that it is his roommate Raheem that shot Sammy. Raheem is obsessed with a Pakistani woman named Farrah who he felt was his property, as they were arranged by their families to marry, and she refused. Raheem never liked Sammy and was extremely jealous of his friendship with Farrah feeling he was coming between them. Farrah, who had been in Pakistan with her sick father, upon returning to NY is brought in by Danny and Jackie to talk to Raheem. She gets him to confess to wanting her to himself and to shooting Sammy to get him out of the way. Realizing this was all just a personal crime of passion and not a breach of security the undercover operations is no longer in jeopardy; they are able to abort the attack which was a bioterrorism attack on NY water supply. Meanwhile Jamie and Renzulli have been called via 911 a number of times to the home of Melissa Samuels, who claims someone has been moving stuff around in her apartment. Although Renzulli thinks she is looking for attention, Jamie empathizes with her and gives her his cell number in case she needs anything. Erin looks into Melissa's story for Jamie, turns out her parents were killed in a private plane crash and she was the only survivor; later being committed for 8 months to a mental health facility for acute anxiety. Upon her next 911 visit Melissa slips Jamie a key, unbeknownst to Renzulli, and asks him to check on her apartment while she is out of town for a week. Later she texts him that someone is in her apartment and she cancelled her trip. Jamie arrives and knocks out the intruder who turns out to be Melissa's brother. He was trying to make her go crazy, and declared incompetent as he is next of kin, and was cut out of parents will.