Myka and Pete go to the Union Station in Denver, CO, to recover the Golden Spike. Pete goes in as a worker to remove a plaque and get at the spike buried in the wall. As she stands watch, Myka spots a man from her past; Leo Bock, the counterfeiter who shot her partner Sam Martino three years ago when she arrived late to back Sam up. Myka goes after him while Pete reaches into the alcove. He cuts his glove on the spike and a cloud of rock dust springs out and starts choking him. Myka has no choice but to go back and neutralize the spike, saving her partner's life. When he notices that she's distracted, Myka says that she almost had the man who killed her partner.
Steve and Claudia go to a farmhouse in Wisconsin to collect a doorknob from Ms. Hodgson. Her great-uncle had OCD and collected doorknobs. Once she goes to get them some iced tea, they look for the artifact doorknob that came from a factory where there was a fire. Steve rips open his glove on the doorknob and dunks his hand in the iced tea as Mrs. Hodgson. As they leave, they notice a dog that comes up to them. As they pet it, someone shoots them with tranquilizer darts.
Pete and Myka go to the station's security room and she explains that Myka was a counterfeiter who stole plates from the Denver Mint three years ago. They check the surveillance footage and spot Leo going out the northeast exit. Myka realizes that he took a bus and insists that she knows everything about the counterfeiter, but he escaped her again. Pete suggests that they contact Myka's old Secret Service team, and she worries that they might blame her for getting Sam killed.
Steve and Claudia wake up and discover that someone has stolen the artifact. They remember seeing a nearby car just before they were drugged, and call Artie. He takes an interest in the dog and tells them to bring it back with them.
The agents go to the Secret Service HQ and Myka sees the memorial to fallen agents, including Sam. As she remembers being with him and his telling her to focus, Myka tells Pete that Sam always had a backup plan. Pete knows that Myka was with Sam, and she explains that Sam had been separated from his wife for a year before they got involved. Myka's former teammate, Zach Adanto, arrives to greet them and explains that he's now the Director of Investigations, the position that Sam would have been up for if he had lived. They meet with Myka's other former teammate, Jim, and go over Leo's files. The agents figure that Leo is back in Denver and Myka realizes that he's going back to the mint to get a new set of plates. He's wearing tourist clothing to blend in on a tour bus and gain access to the mint.
The four agents arrive at the mint as the tour bus arrives. Myka takes command and Leo spots her. He jumps off the top of the bus and shoves past Jim, and then runs into an alleyway. However, when Pete runs into the dead-end alley, there's no sign of Leo. Myka blames Pete for letting Leo get away.
Once they make sure that Jim is okay, Zach tells Myka not to take out her frustrations on Pete. Meanwhile, Pete times how long it would have taken Leo to get out of the alleyway by using a parked truck to get over the wall. They synchronize their watches, time it, and realize that there's no way that Leo could have gotten over the wall before Pete entered the alley... which means that an artifact must be involved, and that Leo used it three years ago to get away from her. Myka goes back to Sam's office to check his old files and look at them as a Warehouse agent rather than a Secret Service agent.
Artie takes Claudia and Steve into the warehouse and shows them a pair of fezzes belonging to Mr. Mental and Coco. Mr. Mental used Coco in a mind-reading act, after building a crude MRI device into the fezzes. They plan to use the fezzes to get the license plate from the dog's mind, but Artie warns that there's one small downside.
As Myka goes through Sam's files, she finds his Secret Service pin and an appointment book with a date for a dinner with her marked. She remembers Sam asking her to dinner and giving her a card, saying that it's a game changer. Zach tells them that they have a tip on where to find Leo and Sam says that he'll take Myka as his backup. Jim comes in and she asks him about the card. He doesn't know about it, but says that Sam planned to invite her to move in with him. Jim tells her that Sam's personal stuff went to Allison, his ex-wife.
Myka goes to see Allison, who admits that it was hard for her to accept that Sam had moved on and became involved with Myka. Allison produces the card and asks that Myka bring her ex-husband's killer to justice. Outside, Pete and Myka open the envelope and discover that it has a musical congratulation card that is blank and plays a song that Sam knew Myka hated.
The security detail calls Pete and Myka to notify them that Leo has been spotted at the train station again. They go there and meet with Jim and Zach. Myka begs Pete to stay behind so that she doesn't risk losing another partner. Pete, Jim, and Myka confront Leo, who puts up his hands. Myka blinks and Leo suddenly has a gun and is aiming it at her. Zach shoots the counterfeiter before can shoot back, killing him. As Pete arrives, Myka realizes that they need to find the artifact.
As the police secure the crime scene, Pete tells Myka to focus. She remembers that Leo was left-handed but he's holding the gun in his right. Pete figures out what happened and tells her to blink slowly. He slips around behind her to demonstrate that someone could have altered the flow of time. The agents check their watches that they synchronized earlier and discover that Myka has lost 47 seconds. They call Artie, who confirms that there is a Warehouse file on the U.S.S. Eldridge, the subject of the Navy's "Philadelphia experiment" in the 1940s. The Navy attempted to create a radar cloaking device but only succeeded for 47 seconds. The agents figure that a second person holding the artifact, Leo's partner, could move through the freeze, and that the partner set up Leo so he'd be killed. Despondent that they have no leads and that she failed repeatedly, Myka tells Pete that she's dropping the case.
Artie prepares to don the receiver fez and warns that if the dog's fez is removed, the feedback could destroy his mind. They put the fezzes on simultaneously and Artie barks out the first three numbers on the license plate. However, the renegade scarab artifact burrows through the wall and runs out the door, and the dog chases after it. Claudia and Steve run after it, leaving an unconscious Artie behind.
Pete joins Myka outside in the car and asks if she's feeling better. He asks her what Sam would say, and Myka echoes that Sam would tell her to stay focused and keep her emotions under control. She realizes that the card is a clue and a backup, and that Sam knew she hated the song. If he was there, he would have made her listen to the end. When they do listen to the end, they hear a recording of Leo talking to his partner, telling the man to get Sam under control because he's getting too close. Myka points out that Jim and Zach were the only other agents on the case and says it's time to do something impulsive.
Claudia and Steve go after the dog without success. When she sees Pavlov's Bell among the artifacts, she gets an idea and uses it to summon the dog. However, it causes uncontrollable drooling for 24 hours. The dog returns, having caught the scarab, and they're relieved to see that it still has the fez on.
Pete and Myka go to the Secret Service headquarters and tell Jim to come with them. They visit Zach and accuse him of working with Leo. Zach angrily walks away and Pete draws his gun. Jim yells that Pete has a gun and Zach turns and fires. Once he does, Jim uses the ship's barometer to freeze both of them with the bullet in mid-air. Myka grabs the barometer and realizes that Jim sent Leo to the building and set it up so that he'd kill Sam. They struggle for the barometer, which falls to the ground. As Jim reaches for it, Myka shoves him into the path of the bullet just as the 47 seconds expire. The bullet hits Jim, killing him, and Myka explains to Zach what happened. When Pete asks if she feels better now that it's over, she admits that she doesn't.
Later, Myka gives the FBI a cover story and a copy of the recording while she keeps the original as a backup. She quickly realizes that Pete knew that Jim was the guilty party all along, and he admits that he worked it out at the alleyway. Pete decided to let Myka walk through it because it was her case to solve. Allison arrives and thanks Myka for bringing Sam's killer to justice. Myka gives her Sam's Secret Service pin and says that it's from her and Sam.
Artie finishes getting the license plate numbers and Claudia confirms that it's a rental. Meanwhile, the dog licks Artie, who explains that they can't take it back because his psychic bond is too strong with Trai. Claudia runs the license plate of the woman who rented the car, and they discover that it's Sally Stukowski, the FBI agent who stole the Van Gogh painting from Steve and Artie in New York City.