A woman who looks as though she's sick exits an airplane restroom. She passes by a man who is sweating profusely while muttering unintelligible words. The guy freaks out. He pulls a gun. BANG! BANG! BANG! Bullets rip through the plane's cabin. The aircraft is going down. On the ground, Megan is on a date with Dr. Charlie Stafford (guest star Luke Perry). The two of them are making plans to go home together when the airplane crashes taking out a power grid. The city of Philadelphia is plunged into darkness.
Megan and Charlie arrive at the crash site. Many are wounded. Many are dead. The tail of the plane crashed in a yet to be determined area. Charlie orders the emergency medical responders to set up a makeshift morgue. The gunman who shot the plane out of the sky is dead. He's identified as an air marshal. Megan believes he may have had a seizure. She brings the body back to the lab while Tommy searches for the tail of the plane with Riley. He's leaving a message on Megan's voicemail when a plane crash survivor appears in the middle of the road. Tommy swerves to avoid her. CRASH!
Back at the ME's office, Kate is shadowed by a reporter who was sent by the D.A. to make her look good. She reveals to a worried husband that his flight attendant wife is not on a list of the dead. Megan believes the air marshal may have been drugged. Interviews with the survivors indicate that a young boy who was flying alone bumped into the gunman. Other witnesses say the air marshal was fixated on a woman-Carla Mendez. A short time later, Megan checks her voicemail. She hears Tommy's crash and is visibly shaken. The only thing that calms her is the fact that Adam is heading out to look for him. Too bad he gets trapped in an elevator with Kate.
The backup generator at the ME's office is down. Megan and Charlie use flashlights to see that Carla Mendez's body has been stolen. The office is locked down. Curtis and Ethan see that someone has deliberately cut the generator power wires. In the elevator, Adam lets Kate know why he's been so hostile toward her lately. It's because he fears she'll go down the same sketchy political road as his father did. Adam opens the elevator car's roof to find Carla Mendez's missing body dangling from above.
Carla Mendez was a drug mule who had 80 bags of cocaine in her stomach. Her accomplice stole her body to get the drugs. Elsewhere, Tommy and Riley are banged up, but able to walk. They find the injured flight attendant, Pam, in the middle of the road. In the distance, there's the smoldering wreckage of the rest of the plane. Tommy finds Max, the young kid who was flying alone. Riley grabs the flight attendant's purse. Tommy uses her phone to call Megan, who is overjoyed to find out he's alive. Charlie sees how much she cares for him.
The flight attendant's worried husband, Alex, is thrilled to learn that his wife is alive. Megan talks Tommy through an emergency tracheotomy to keep her that way. In other news, Adam finds a bag of cocaine on a passenger. He promptly arrests the guy believing he's the one who was in cahoots with Carla. In reality, Alex is the one who is dealing the cocaine. His flight attendant wife is the one who drugged the air marshal not realizing what kind of reaction it would have on him. Adam is able to arrest Alex before he can escape with the stash of drugs he cut out of Carla's body.
Tommy places the injured flight attendant under arrest at the crash scene. He gets some advice from this woman about choosing the right person before she's taken away. The young boy, Max, is sent off to be reunited with his family. As for Megan, she lets Charlie know that she needs to be with Tommy. Too bad she arrives a little too late. Tommy heads out of the precinct with Riley. Megan leaves as well, alone and defeated.