It's dawn when the computers in a high-tech lab go crazy, every monitor yielding the word "Ivan." Engineer Nathan Platt rips the network's connective wires out of the wall and hits the street, making a call to report the network has been breached. He's heading to the backup site with the prototype when a hacker with a laptop sets off the airbag in his car. The ensuing crash kills Nathan handily. Meanwhile, Red meets Mr. Kaplan in the woods at the excavated grave of The Cowboy and Jolene. After instructing Mr. Kaplan to put everything back exactly as he found it, Red calls in a missing persons report on Jolene.
Liz has just gifted Tom an Uncle Flippo flashlight when Detective Debarros knocks on the door looking for Jolene and making Liz late for a meeting with Red. He hands her a photo of Nathan's crash, blaming notorious Russian cyber criminal Ivan who incidentally stole millions from him. Ivan already took credit for the murder in a deep recess of the Internet, and oddly this is the first time he's struck on U.S. soil. After asking Aram to access Jolene's phone records, Liz and Ressler proceed to the police impound yard to check out Nathan's car. Aram quickly figures the airbag deployed before the crash, and Ivan has left a digital signature. Liz has just found an empty RF-shielded case when the NSA drives up. Cooper rushes to the scene to sort out the red tape; Nathan was NSA, lead engineer on Project Skeleton Key, the prototype able to take control of any system with the push of a button. Headed by David Fisher, the operation was about to be moved to Colorado, and now the prototype is missing. Liz visits Red, who knows Ivan is in Minsk. Advising Liz that the only way to get Ivan's cooperation is to create a problem they can solve, Red and the FBI board his jet. Red offers to let Ivan repay the money he stole with interest, in exchange for an escort out of the FBI sting that's about to go down. After he gets his money, it doesn't take Red long to discover Ivan knows nothing about the Skeleton Key; in fact, someone else has been using his digital signature.
Back at the FBI, Aram tells Liz that Jolene's last outgoing call was to her, while Ressler and Meera start tracking whoever's been posing as Ivan. The trail leads to Ruby Lee, the beneficiary of a Social Security hack. Ruby is unaware that her payments were increased; she's completely reliant on her 17-year-old grandson Harrison for all things digital. Meanwhile, Liz has tracked down the address of Tom's safe house. Standing outside, she calls him. Tom pretends the call is breaking up, then jets into motion, burning everything. Liz enters the building and a game of cat and mouse ensues. Tom is able to body check Liz without being seen and flees the building to call his handler with a message: "Tell Berlin I was forced to liquidate." Within the hour, the safe house has become a crime scene. Liz asks Debarros to keep her looped, then runs off to meet Ressler and Meera at Harrison's high school. Harrison is busy stalking fellow student Abby when the FBI arrives. Using the Skeleton Key to set off an evacuation drill, he's able to escape. Back at the FBI, Aram has learned Harrison was stalking Abby Fisher, daughter of David, head of the Skeleton Key project. They've just got David on the phone when all the power in D.C. goes out. Harrison activated the Skeleton Key!
Posing as a girlfriend, Harrison texts Abby, convincing her to meet in a D.C. metro station. Aram triangulates his location, and the FBI rushes to the scene, as Harrison explains everything to Abby: knowing she didn't want to move to Colorado with her father, Harrison stole the Skeleton Key so she wouldn't have to. Trying to get away, Abby freaks out and falls, knocking herself out. Just then the FBI arrives, sending Harrison running for a subway train. He manages to activate the train, just as Liz jumps onboard. The train speeds towards a crash. Knowing Harrison is the only one who can stop it, Liz talks him down. When it's all over, Liz returns home to go over her Jolene file as Tom cooks dinner. When she spots Uncle Flippo in a photo from the safe house crime scene, she finally knows in her heart what Red has been suggesting all along: Tom is not who he says he is. Liz retreats to Red's workshop, where he presents her with a music box, which plays a song her father used to sing to comfort her. Red knew Liz was about to discover the truth about Tom... and he wanted her to know everything is going to be okay.
While chasing a cyber-terrorist, Liz investigates Jolene's disappearance.