Pig farmer Casey complains when Dr. Everett Udall is overstaying his rental agreement. Udall apologizes for the delays and then has his henchman grab Casey and inject him with a hypo.
In Congressional hearings, Colonel Michael Vance informs the committee that he conducted a successful operation. However, Senator P.J. Young complains that Vance assembled a team in violation of government protocols. He refuses to hear Vance's defense that they need an asymmetrical team to cope with terrorists and warns him that he'll be in violation of Federal law and imprisoned if he does it again.
In Washington, Parker, Hardison, and Eliot break into the Castleman company's security vault and take out the guards. Hardison shuts down the motion sensors but is unable to deactivate the laser grid. Parker refuses his kiss for luck, saying she doesn't need it, and then twists her way through the laser beams to the deposit vaults. She then uses a miniature blowtorch to open a vault and remove a case of diamonds belonging to Prime Minister Entebbe.
The trio gets outside and calls Sister Agnes to tell her that the diamonds are on their way. Parker wants to keep just one but Hardison reminds her that they're good guys. Eliot gets a call from an old associate, Riley, who has heard that Eliot is in town and wants him for a job. The hitter refuses, saying he doesn't do that kind of thing anymore. Riley hangs up but Eliot realizes that the man would have a backup already in place to make the kill.
A little later, Eliot enters Riley's office and demands to see the file on the target. Riley wonders why he quit and Eliot tells him that he's running with a different team. When Riley goes for his alarm, Eliot tells him that he has a hacker who disabled the alarm. Riley goes for his gun only to discover that Parker has removed the bullets. Eliot repeats his request and Riley hands over the file. After Parker tasers Riley unconscious, Eliot confirms that the target, Teresa Darnell, is going to be hit in 15 minutes while getting off the train at Greer Park.
When the team gets to the station, Eliot checks the area and figures that the killer will have to take a shot with a rifle from the building behind them. He goes to stop the killer and tells Parker and Hardison to get Teresa out. When she comes out, Eliot approaches Teresa, blocking the shot, and then carries her to cover. Hardison whips together a smoke bomb out of an aerosol can while Parker steals a motorcycle and takes Teresa to safety. Eliot goes up into the building and intercepts the sniper on the way down, taking the man out.
The team meets up after sending Teresa on her way. Eliot confirms that she's a 911 emergency administrator in Washington and figures that it's a terrorist attack. He decides to call an old friend in CTU: Vance. Once he warns him, Vance asks for a meeting back at the train station. As they go back, Eliot explains that he and Vance used to do wetwork missions for the government back in the day. When they get to the station, Vance immediately has his men arrest them. He then takes them into a van and leaves, unaware that Senator Yount is watching.
Once they're away from the station, Vance tells Eliot that he knows about Hardison and Parker. He explains that terrorist have hit two other administrators in the city as part of an effort to cripple the city's infrastructure prior to an attack. Vance admits that it will take too long for him to put together a team and he's under Senate scrutiny, so he needs Eliot to do the job for them. He'll drop the charges and loan them a NSA intel van. They agree and Eliot knocks Vance out to make their escape look good. They head back to the station and Parker hot-wires the van while Hardison convinces the agent on duty that he built the van and they need to drive it away before the power lines scramble the database. Once they're inside, Parker drives off in the van.
Once they're clear, the team stops and Hardison checks all of the intel resources in the van. Eliot insists that he wants them out of the way but his teammates remind him that they agreed to change... together. They go to work and Hardison checks the databases for info on the killer's fingerprints. Eliot narrows down the search by confirming the man was a former Navy SEAL from the type of watch he wore. Hardison identifies the man as Charlie Scalzi and then runs a check on his credit card use with parking meters. Scalzi visited the same area eight times several months ago, and there was a jewel store robbery across the street. According to the news reports, the robbers hid in the basement of an antique store and brought a cooler of drinks with them. Parker realizes that the cooler is the key and says they need to get to the antique store.
Udall, disguised in Arabic clothing and posing as Ahmed, drops off a package at the Washington Union News office. He tells the secretary that the editor will want to see it immediately and walks away.
The team goes to the antique store and Parker explains that the robbers used the ice in the cooler to cool down the saw blade they used to cut through the basement wall. She breaks through the wall and they find a long-abandoned bio lab on the other side. Hardison confirms that the facility used to be the Coldwater Health Science Foundation, a precursor to the CDC, and was shut down in 1934 and subsequently forgotten. Eliot finds an opened case labeled Influenza – 1918, and a panicky Hardison tells everyone to get out immediately. When they get outside, he explains that the Spanish Flu killed fifty million people in 1918 and the fatalities were only limited because of the population. The death toll if it were released in the present would be ten times that. Hardison panics, insisting that they're in over their heads, but Eliot tells him that he has the best thief and the smartest guy he knows helping him and that's all he needs. After a moment, Hardison gets a grip and tells his teammates that their target will have to weaponize the virus and will need pigs.
When they get back to the van, Hardison checks the database while explaining that influenza starts in animals and then jumps to humans. He finds the Casey farm and confirms the owner shut it down three weeks ago. Eliot calls Vance, who tells them that they've received the terrorist manifesto left at the newspaper office. However, Vance warns them that they need something definite before he can make a move.
When the team drives to the pig farm, they find medical equipment and split up to search the farmer. Parker finds the owner's corpse and Eliot locates a pen filled with hundreds of dead pigs. They call Vance to tell him they have something definitive and Hardison follows the paper trail on the farm rental to confirm that the terrorists own a trailer on the outskirts of town. Vance arrives and tells them that his people will secure the area, and Hardison tells him that fire is the only sure way to eliminate the virus. Vance calls in his assault team to take out the terrorists at the trailer and tells Eliot and the others that they're off the hook.
As Parker, Hardison, and Eliot, they realize that something isn't right. Eliot points out that the terrorists only targeted one hospital administrator instead of each one at a hospital in DC. They figure that the three targets had something in common and Hardison uses the database to confirm that they all attended a symposium on bio-terrorism in Berlin three years ago. Dr. Everett Udall was the guest of honor and Hardison runs down his DC address, figuring he can help them if the terrorists haven't already killed him.
Vance takes an assault team to the trailer and they close in. Senator Yount arrives to oversee the operation and asks if Vance has a warrant. The colonel admits that he doesn't and tells his men to get one as soon as they can.
The team goes to Udall's address and Hardison goes in first. He stops just in time, realizing that he's stepped on a pressure trap, and spots the claymore mine on the floor in front of the door. The others refuse to abandon him and Parker climbs over his shoulders, hugs Hardison, and then lowers herself backwards, assuring her boyfriend she doesn't need luck. She disarms the claymore and they realize that Udall is the terrorist. They check his computer and confirm that he was fired from CDC when he became obsessed with the threat of biological terrorism. There are also plans for a gas bomb that will spread the virus across DC. As they find all of the information, Eliot realizes that everything is there and figures that the trailer is a trap.
Vance and his men close in on the trailer while Hardison tries to call the colonel. The phone is in Vance's SVU and Yount picks it up. He figures that it's a prank call and hangs up, and Hardison hacks into Vance's Bluetooth speaker link. He then accesses the SVU's electrical system and honks the horn in SOS Morse code. Vance hears it just as he prepares to open the door, realizes that Hardison is warning him, and pulls his men back just in time as the trailer explodes.
At Udall's home, Parker checks the refrigerator and discovers that it's full of eggs. Eliot figures that Udall will deliver the bomb to somewhere with huge crowds and Hardison tracks the doctor's GPS phone tracer. He locates Udall in the subway and they drive there. However, between the crowds, the wiring, and the concrete, Hardison is unable to pinpoint Udall's location.
Udall, unaware that he's being pursued, boards the subway train and it departs. Hardison confirms that the signal is on the move and tells Parker to get on it. She's already on the train heading for the forward car, and Eliot and Hardison go outside, steal a car, and drive for the main terminal. A patrolman spots them and pursues, calling in for reinforcements. Hardison confirms that there's a maintenance tunnel at the next bend in the tunnel and Parker, working against the wind resistance, manages to drop to the side and hits the emergency break. Hardison and Eliot enter the maintenance tunnel, locking the door behind them, and head for the train.
As Parker enters the train and tries to spot Udall, Eliot figures that he'll be the one who is nervous. However, Hardison realizes that Udall was using the eggs to create a vaccine culture and he'll be the only one on the car that isn't panicking. As Parker moves through the car, she bumps into Udall and notices him wince when she hits his arm. She points out that he must have recently had a vaccine shot, and Udall draws a gun. He yells that the government has to wake up and realize the threat that biological terrorism poses, and he plans to show them. As Hardison and Eliot get the passengers off the train, Udall reaches for the briefcase containing the viral bomb... only to discover that Parker has stolen it. Eliot charges at Udall, who shoots him in the chest before Eliot can drop him.
Hardison opens the briefcase only to discover that there's a glass plate covering the bomb, and cutting it at the edges will set the bomb off. Parker produces the one diamond she kept from the earlier robbery and uses it to cut a hole in the glass. While Hardison tries to disarm the bomb, Udall wakes up and grabs the gun. Hardison disarms the bomb but warns the others that there is a secondary aerosol delivery system that will spray the virus out of the case, releasing enough influenza to kill everyone in DC. Udall opens fire on them and the team ducks for cover.
With time running out, Eliot and Parker realize what they have to do. Eliot charges Udall, blocking the bullets with his own body, and taking the man out. Parker grabs the briefcase and runs down the track. Hardison runs after her, begging her not to do it. However, Parker uses the miniature blowtorch from the break-in to burn the virus as the aerosol sprays it out of the case, destroying it once and for all. Hardison runs up and hugs her, saying that he can't handle losing her.
Later, Vance and his team secure the area and take Udall away. The colonel wants to recruit Eliot as part of a CTU team. However, the hitter points out that Vance is almost as obsessed with getting the government to see his point of view as Udall is. As he limps off with his friends, Eliot says that he's got his own team of bad guys to work with.