Mac is on a flight to Washington, D.C. to testify in a trial, when he notices the stewardesses convening in the back of the plane. He goes to see what's going on, and, after he flashes his badge, they show him the cause of their distress: a dead man in the bathroom, the victim of a fatal stab wound to the carotid artery. Mac discovers a badge identifying him as a Federal Air Marshal and notices his gun missing. Mac gets the pilots to turn the plane back to New York, and enlists the one man he knows is innocent--the passenger next to him, Ed Riley--to keep an eye on the cabin while he examines the body. There's no ID on the body, so Mac asks the flight attendants to contact the FAA to get an ID on the Marshal assigned to the plane. One of the flight attendants, Susan, recalls a passenger, James Turner, who was agitated during the flight. Mac takes a glance at the man and notices blood on his sleeve. The mystery deepens when the other flight attendant, Nina, relays startling news to Mac: the dead man on the plane is not the Air Marshal who was supposed to be on the flight. Mac fingerprints the man using Nina's lipstick and an airsickness bag, then using a borrowed satellite phone from one of the pilots, takes a picture and sends it to Stella, who puts Lindsay on the case. Lindsay gets an ID: Anton Greenway, who escaped from custody the day before after a major drug smuggling conviction. Danny and Flack track the real Air Marshal, Roger Stockwell, to a hotel room, where they find the man dead on the floor, the victim of a gunshot wound to the head.
The plane lands and Stella tells Mac Homeland Security gave the go-ahead for him to take the lead on the case--but without warrants, they can't detain anyone on the plane for any longer than 24 hours. Mac questions James Turner, immediately suspicious of the man. On the plane, Stella and Hawkes discover Anton's real reason for being on the plane: a bag full of Canadian money. In the morgue, Sid shows Lindsay that a bruise on Stockwell is a match to Anton's fist, strongly suggesting Anton was responsible for the Marshal's death. The coroner also discovered traces of lubricant on Anton, as well as letters written on one of his hands. The blood on James Turner's shirt turns out to be his own, eliminating him as a suspect. Lindsay works on the letters on Anton's hand and deduces they're coordinates for an airfield in Montreal. Anton was likely planning to hijack the plane and take it to Canadian airspace. While Hawkes discovers that Anton's jacket had deep hidden pockets to conceal the cash, Danny gets a hit off a print on the gun used to kill Roger Stockwell: a club manager named Terrence Davis who was busted for drug running and used to work alongside Anton Greenway at Atlantic Vista airlines. Flack and Danny go to Terrence's club where the owner admits to seeing Anton the day before but denies he's in league with him. When he goes to show them his gun, he's shocked to find it missing. Flack arrests him on a parole violation and, once Terrence's alibi checks out, agrees to let him take a plea bargain from the DA in exchange for being an informant.
After sifting through trash and human refuse, Adam discovers a condom wrapper with lipstick on it. Stella and Lindsay try to identify the murder weapon from two prong marks on Anton's jaw to no avail--until Mac notices a picture of one of the flight attendants wearing a wing pin. The pin's prongs are a match, and Mac scans the pictures, discovering only one flight attendant missing her wings: Susan. Flack makes a quick call and discovers Susan is on a flight to Paris. He and Mac rush to the plane with just seconds to spare and catch the woman. Blood on her wing pin is a match to Anton. Susan admits to planning to run away with Anton and the sizable amount of cash he'd stolen, but when she found out he'd killed the Air Marshal and after he threatened her with a gun when she refused to help him hijack the plane and take it to Canada, Susan turned on him and stabbed him with her pin. Rather than claim to have stopped a terrorist, Susan concealed the crime, hoping to get away with the money. Mac notes that she made the wrong choice--and now she's grounded for good.