At the Bee Meadow Winery outside of Portland, worker Sam Knox collapses. One of his co-workers, Betty Carter runs over to help him but the head foreman, Leonard, tells everyone that Sam is fine and orders them back to work.
Sometime later, Sam's daughter Kirstin meets with Nate and explains that after her father died of heart failure, a lawyer from the winery offered her $1,000,000 if she would sign a non-disclosure statement. Nate figures that the winery owner has something to hide and promises Kristin that they'll find out what that secret is.
Eliot goes undercover at the winery and watches as Leonard drives by, ordering everyone to pick up the pace. Once Leonard leaves, Betty comes over and warns Eliot about the foreman. As they share a bottle of water, Eliot asks about Sam but Betty quickly turns and leaves. Eliot then check sin with Nate, who tells him to find out what he can about Sam. Meanwhile, Hardison and Sophie go over the non-disclosure statement and figure that the winery has paid off other relatives in the past.
Parker poses as an intern to get into the winery and chats with her fellow interns, while Sophie explains to Nate that she's been giving the thief tips on internalizing her undercover roles. The owner, Frank Madigan, arrives and tells the interns that they'll be working as janitors without pay in return for college credits, and he plans to boost the production tenfold. Parker is less than happy and Sophie has to remind her that she isn't actually an intern. Meanwhile, Hardison checks Madigan's background and discovers that he bought the winery, fires the staff, and hired part-timers. Madigan used to run a chemical manufacturing plant and there were several accidental deaths at that plant as well.
Nate wonders what Madigan has planned and checks the financials. He discovers that Madigan took out a loan to buy the winery using his wine collection as collateral. The rarest bottle in his collection is a bottle of wine that belonged to Thomas Jefferson. Sophie is eager to steal it but Nate warns that since it's insured, stealing it would simply get Madigan a big insurance check. What the team has to do is make Madigan's collection worthless. Once they do, the bank will cancel the loan and Madigan will lose the winery.
Hardison ends up going in as a vintner even though he warns Nate that his specialty is beer, not wine. To get Hardison in, Sophie poses as a blogger and meets with the winery's previous vintner. She gets him to describe everything he did and then sends it to Hardison, who takes the opposite approach with Madigan. The owner quickly hires him and introduces him to the interns. Hardison insults them, much to Parker's disgust, and then has his computer brought in. He explains that he's going to put in CO2 monitors and sends Parker to find some parts, giving her plenty of time to look around. Once she's outside, Parker finds Eliot and they spot Leonard going by.
Nate and Sophie go over her part of the plan and he warns her that Madigan know wine at a molecular level and will be hard to fool. Sophie assures Nate that it's a matter of status, not knowledge, and that there's fake and then there's fake. Nate asks what the difference is but Sophie just walks away. She then goes to the winery where Madigan is hosting a wine-tasting and asks to work for him as a pourer. He refuses, telling her to go to HR, but Sophie offers to sell a case of wine to anyone in the room. Madigan points out that they're just there to sample, not buy, but Sophie persists and he tells her that he'll have to sell a case of wine to... him.
Eliot and Parker check the fields for the cause of Sam's death but there's no obvious indicators. Leonard goes by and Eliot figures that he's tough but he's not killing his workers. As Parker and Eliot talk, Betty listens in from nearby.
Sophie serves Madigan a bottle of his own wine but he's unimpressed and refuses to buy it. She then suggests that the vintner hid a special bottle for the staff and locates it beneath the counter. Sophie wraps a cloth around the bottle and pours it for Madigan, who tastes it and is impressed. She then shows him that it's the same bottle and explains that she psyched him into believing that the second bottle would be better than the first. Impressed, Madigan hires her and explains that he plans to produce ten times the wine that the previous owners did at half the price. It won't be as good as what his predecessors made, but it'll be good enough to sell and he wants Sophie to help him.
Parker and Eliot check the fertilizer canisters and discovers that they have fake labels and there is some other substance inside. Parker takes a sample and they report to Nate, who tells them to get it to Hardison. Once Parker drops off the sample, she needs to check the paper trail on the fake fertilizer. Meanwhile, Eliot sets out keep the substance away from the workers and Nate tells Alec and Sophie to begin their swap-and-whisper campaign.
Sophie is selling out wines to the tasters and Madigan invites her up to the ventilation tower. He explains how that it was an early air conditioning system to remove toxic levels of CO2 from the winery, and Sophie asks about his rare wines. Madigan takes her down to his underground cellar and Sophie records everything on a button-cam as Hardison monitors her from his computer in the plant. Sophie finally goads Madigan into showing her the Jefferson bottle and he brings it out. However, he explains that there's a special seal on it and the bottle can't be opened without breaking it. Hardison warns the team that it will take days to duplicate it and no guarantee Sophie can arrange another trip to the cellar. As Parker arrives with Hardison, Nate tells the hacker to make up a fake bottle while he comes up with an alternative.
Next, Nate gives Sophie the go-ahead to begin the whisper campaign. She dismisses the Jefferson bottle with a shrug and moves on, and Madigan wonders why. Sophie explains that her old boss confirmed that the bottle was in the collection of a Saudi prince and that he had it triple-checked and authenticated. Madigan nervously insists that he has the real thing while Sophie plans more doubts by talking about how half of her ex-boyfriend's wine collection was fakes.
Eliot finds a truck of the fertilizer and workers unloading it. He claims that Leonard ordered him to move it, drives the truck away, and then "accidentally" spills the canisters. Meanwhile, Hardison checks Parker's sample and tells the team that it's an experimental fertilizer that causes accelerated plant growth but heart failure in humans. Meanwhile, Parker checks the factory office computer but Hardison can't help because he's busy spoofing Madigan's computer and putting fake stories establishing Nate as Sophie's former boss and a rich Harvard man that will impress Madigan.
Madigan runs a check and sees the fake articles, and decides to call wine auditor Dan Snyder. Hardison intercepts the call but before he can do anything with it, Parker warns him that she's trigged a system wipe. He runs across the factory and manages to stop it just in time, but discovers that Madigan has already deleted the information. However, the logs show that someone else copied it before it was deleted.
Once he gets the news, Nate calls Kristin, brings her up to speed, and asks if anyone else from the winery visited her. Once she confirms that a woman came to see her, Nate has Hardison pull up the security footage. They confirm that Betty is the inside person who stole the data and that she made an anonymous tip to OSHA. Hardison brings up the company files and learns that Leonard put Betty on a suspect list and they figure she's been nervous around Eliot since she figures him for Madigan's undercover man. Parker and Eliot spot Leonard coming and get out just in time. The foreman sees Betty's file on the computer screen and concludes that she's the spy. Leonard meets with Madigan and the owner tells his henchman to dispose of Betty while he meets with Snyder.
Snyder arrives with his high-tech equipment and prepares to test the Jefferson bottle. Nate knows the three tests that Snyder will run and makes sure that Sophie, Parker, and Hardison are in the room. The first test is an optical scan and analysis of the bottle. Sophie steps forward and wishes Madigan lucks, and gives the bottle a kiss for luck. When she does so, she puts a piece of invisible film with a modern-day laser-printed letter on it.
Nate tells the team that the next test will involve an spectrographic analysis to confirm that the bottle has manganese in it. Parker approaches Snyder and Madigan with wine glasses and offers them drinks. Madigan wonders why the intern is there and orders her out, unaware that Parker has secretly slipped a lens into the spectrometer which indicates that there's no manganese in the bottle.
Leonard and two of his men go out into the field and go after Betty, who tries to run away.
For the third test, Snyder uses a Geiger counter to determine whether the bottle has low levels of cesium radiation. Since 1947 all wine bottles have been mildly contaminated because of low-level atomic testing. Hardison has secretly contaminated Snyder's gloves with a radioactive slurry so the Geiger counter shows positive, meaning the bottle is a fake. Nate is satisfied that everything is going as planned... until Snyder declares that the bottle is genuine.
Eliot finds Leonard's tracks and notifies the team that Betty has been abducted. He goes after her while Nate works out that they connect Madigan all too well. He figured that his bottle wouldn't past the tests so he bribed Snyder to ignore the results and confirm the bottle was legitimate. However, when Sophie approaches Madigan, he nervously tells her to go home because he's giving all of the workers the day off and closing the vineyard.
Parker and Hardison get an app readout that Madigan has taken the CO2 monitors offline. They figure that he's going to have Leonard plant Betty in the lower levels, flood the winery with CO2, and when she dies let her take the blame as a botched attempt at sabotage. Hardison confirms that Madigan has shut down the HVAC system so he and Parker head for the top of the ventilation tower to open the door and let the fresh air in. Eliot goes to rescue Betty and Hardison warns him that he'll soon run out of oxygen.
Eliot finds Leonard and his men in the lower vat level with Betty. As his oxygen runs out, Eliot manages to take down the two men. However, Leonard dons an air mask and takes on the weakened Eliot.
Hardison and Parker head up into the tower but two guards move to intercept them. Parker ducks around them while Hardison takes one out and they head up to the top with the remaining guard in close pursuit.
Leonard tells Eliot that he'll be unconscious in thirty seconds, but Eliot tells him that he only needs ten. He grabs Leonard and tosses him into one of the vats.
Parker gets to the top of the tower and tries to open the doors. When the last guard tries to grab her, Hardison arrives in time to knock the guard out and Parker gets the doors open, flooding the winery with fresh air.
Eliot finds Betty and makes sure that she's okay. As he carries her out, Nate says that they've got a win and Eliot wonders why. Nate figures that Madigan knows that he has a fake bottle of wine and will try to get rid of it before word inevitably spreads.
Soon, Madigan contacts Nate and offers to sell him the bottle off the books. They meet in the vineyard and Madigan explains that he's temporarily closed down the winery because of a misunderstanding with OSHA. However, as soon as Nate pays Madigan for the bottle, the FBI step out and arrest Madigan for fraud. Nate explains that Snyder confessed to the fake authentication and they have everything they need against Madigan. The FBI agent lets Nate keep the wine because it's (supposedly) a fake, but Madigan realizes too late that he had the real wine all the time... and now Nate has it.
Later, Nate meets Kristin and Betty at the restaurant and gives them the evidence they have on Madigan. Betty assures Kristin that her father was a good man. She also thanks Nate for giving them enough money to let the employees buy the winery and run it themselves. Nate steps away and Sophie asks where he got the money. He tells her that he sold the Jefferson bottle and then pours two glasses for a toast. Sophie admires the wine and then realizes that Nate said that he sold the bottle but didn't say anything about the wine. She wonders if the buyer would know but Nate points out that if hypothetically he did sell the bottle, the buyer would never open it and find out. As Sophie wonders if Nate actually kept the wine or not, he tells her that he knows what's real and what's fake.