In 1997, NYPD detective John Corey, is on the back pourch of his uncles waterfront home on the North Fork of Long Island recovering from three gunshot wounds while working in his town of Manhattan, NY. He enjoys that the tourist season is just about over so that its just him and the locals. He listens to music while sitting in a chair and using binoculars to spy on people in a distant boat enjoying themselves.
The local police chief Sylvester Maxwell comes to the back porch and asks Corey to act as consultant in a local murder investigation, as Corey is personally acquainted with the two victims, Tom and Judy Gordon, both employees on the Plum Island Animal Disease Center, a facility suspected of carrying out biological warfare research. They go to the rented house the victims are at a waterfront property that appears to have been robbed or searched and the two victims have been shot in the head on their own dock. Corey concludes that this wasn't a robbery gone bad due to valuable objects in plain sight, he also says that the victims were near their killer because its hard to him a person in the head with one shot at a range. They cannot find the bullet shells to tell what type of gun it was and by the direction of the wounds conclude that the bullets are in the bay.
Max is unhappy because of the fact that because he's not a homicide detective his expectations of Corey's findings were high. Beth Penrose - the police detective from the next county over - arrives, Corey instantly figures out she's in charge of the case without her stating it. She yells at him a bit for being on the crime scene because he appears to be a civilian, he ignores Beth and searches the Speed boat that the Gordons temporary docked. When he gets out of the boat she pulls his gun on him and makes him state who he is. Just before he goes he asks if they found the chest in the boat that the Gordons used as a trunk while boating, they reply that its missing. Corey goes to the local bar an orders junk food he is watching the game as Beth comes in and tries to be nice to him in an attempt to get the info out of him. Corey responds by rudely calling bullshit on her and agreeing to an interview next day she invites him to come back with her to see the government agents involved.
Later he comes back to the crime scene, into its kitchen and sees George Foster, an FBI agent, and Ted Nash, who claims to represent the Department of Agriculture but whom Corey immediately recognises as a CIA due to being at a crime scene at the late hour. They discuss theories of the deaths as the Gordons trading the deadly diseases they have access to for money and using the boat chest as a container for the items.
The TV shows news of the murder and exaggerates the importance of the Gordons' work in order to make it look like two scientists were murdered, possibly to make it more dramatic. Corey silently dislikes how the reporter exaggerates it because there is no public evidence of the work connecting them. Corey is jealous of the younger Beth liking Ted Nash, the two clash over who is the alpha male of the room, Corey is able to get Ted to make himself look like an ass to Beth. Beth Corey and Max are able to make Ted cave in to letting them go on Plumb Island the next day.
Corey then goes through the Gordons' book shelves and pulls out a map of the local boating water. He notices a mysterious code written on one of the pages. The next day he arrives early at the ferry station and sees George and Ted with the security director and other people in suits coming off of the ferry, confirming his thoughts of a cover up. They do not see him and he gets on the ferry to Plum Island with the rest of the group from last night with Paul Stevens the security director, who pretends he doesn't know George or Nash. They are brought to the island and given a bus tour of it as Paul pretends to be nice to them. The group then walk through the long hallways with the head of the research center who has some humor but feels like hes on a script. They are shown a few scientists who are friends of the Tom and Judy who were directing a project.
The scientists act like they are on a script and give cover up theories that suggest they were underpaid government workers who stole a vaccine so they could "discover" it elsewhere and become rich and famous. Corey asks if he can go to the level five area but is denied because he is under-prepared for it and will get sick and probably die.