At the Casey Pig Farm in Virginia, the farmer approaches Dr. Everett Udall, who is running tests, and points out that the three-month rental agreement was over two weeks ago. Udall says that there have been delays and has his man grab the owner, and then injects the owner with a hypo and walks away.
On day 6 of the Congressional hearings, Colonel Vance gives a report on a successful operation. However, Senator P.J. Yount complains that the team he assembled to take out a terrorist bomb maker was put together from different agencies in violation of police. Vance defends his actions but the committee finds him in violation of Federal law and warns him that if he assembles another team then he will be in jail.
At the Castelman security vault, two guards are on duty and hear the elevator coming down. They get no response from security and watch as the doors open. Alec is standing there and Eliot comes up behind the guards and knocks them out while Alec finishes overriding the cameras, Parker drops down from the ceiling. They get the vault open and Parker slips in past the security laser grid. She then cuts open one of the vaults and removes the hidden diamonds belonging to Prime Minister Entabbe.
Outside, Alec calls Sister Agnes and tells her that they have what they came for, and then calls to tell Nate that they're finished. As the trio takes off, Eliot gets a page from an old "friend," Riley. Riley says that he has a job for him in town and Eliot says that he doesn't do that kind of thing anymore. Eliot's contact hangs up but Eliot tells his teammates that someone else is doing it if he isn't.
Riley calls in his security guard and warns them that they have cash coming in. Once the man leaves, Eliot steps in and says that he can't let it go down and asks to see the file. Riley asks why he quit and Eliot says that he's running with different people. The man discovers that Alec has disabled his alarm and Parker has removed the bullets from his gun, and Eliot repeats his request for the file. Riley hands it over and Parker tasers him unconscious. The file shows that the target, a woman, gets off the train at Greer Park in 15 minutes.
The trio head for the station and Eliot figures that the killer will take the shot from the roof behind. He tells Parker and Alec to get her out while he stops the killer. The woman, Teresa, emerges from the station and the sniper draws a bead... and Eliot blocks the shot and asks Teresa for directions. He then picks her up and carries her to cover while the sniper opens fire. Parker steals a motorcycle and Alec creates an improvised smoke bomb for cover. They get Teresa on the motorcycle and Parker drives away with her, and Eliot goes up the building and intercepts the killer. They fight and Eliot takes the man out.
Once Parker is clear, Eliot checks with Teresa and confirms that she's a 911 administrator in the DC area. Eliot figures that it's a terrorist attack and calls his old friend, Vance. Afterward, Eliot tells Parker and Alec that he and Vance were in the service doing dirty work for the government. Vance meets them and Eliot brings him up to speed. The police surround them and Vance puts Eliot and the others under arrest. The colonel gets them into a van and takes off, while Senator Yount watches.
Once they're alone, Vance reveals that he knows about Alec and Parker and explains that several leading administrators have all been killed in Washington. Eliot figures that terrorists are crippling the infrastructure in anticipation of an attack and Vance explains that it will take too long for him to put together his own team. He offers to drop all the charges against them if they can stop the terrorist attack by that afternoon. Vance offers them a mobile NSA intel van and tells them to make their escape look good. Eliot knocks him out and Parker gets the door. They go back to Greer Park and Parker boosts the van while Alec tells the agent that he built the truck and warns that it can't be near the power links. They bluff the agent and get inside, and Parker drives off.
Once they're clear, Alec checks all of the systems and is duly impressed. Eliot says that he wants them out but Alec says that he'll need their help and Parker says that they agreed to change together. They start by checking the fingerprints on the killer, and Eliot tells them to check Navy SEAL records because he recognized the man's watch. Alec confirms the man is Charlie Scalzi and checks his parking records. Scalzi checked on the same block eight times several months ago and Alec checks on the nearby buildings. He comes up with information on robbers that hid in an antique store before robbing a jewel store. The report says that they had a cooler and Parker says that the cooler is the key.
At the Washington Union News office, Udall, disguised in Arabic clothing, drops off a package and tells the secretary that her editor will want to see it.
Parker drives to the antique store and checks out the basement. She finds where the supposed robbers painted over the wall and explains that they used the ice in the cooler to keep the saw blade cool as they cut through. She breaks through the wall and they find a bio lab on the other side. The facility belongs to the Coldwater Health Science Foundation, a precursor to the CDC, and was a privately funded government research facility shut down in 1934 and forgotten. Eliot finds a case containing influenza samples from 1918 and Alec immediately tells everyone to get out. He explains that the Spanish Flu killed fifty million people during World War I. Outside, Alec insists that they can't handle it and he's scared, but Eliot says that he isn't because he's got the best thief and the smartest guy he knows chasing the guy. Alec figures that their target will have to weaponize it and he needs pigs.
Back in the van, Alec runs database checks and explains that the disease travels through animals first and then jumps to humans. He calls up NSA records and finds a farm that the owner shut down three weeks ago. Eliot calls Vance, who informs him that "Ahmed" dropped off a letter at the newspaper and wants Eliot to report back in with he has something definite.
The team arrives at the pig farm and finds medical equipment. They split up to secure the area and Parker finds the owner's corpse. Eliot calls them over to the pen filled with hundreds of dead pigs. Eliot calls in Vance and turn over the lease agreement that they found for a trailer. The terrorists used five shell companies but Alec has come up with another lease. Vance figures that it's time to send in an assault team and Alec tells him to burn it because fire is the only way to kill the virus. The colonel tells Eliot and the others that they're cleared and to drop off the van.
Back in the van, the trio wonders why they're not happy that Vance is on the job. Eliot wonders why the terrorists only killed one hospital administrator, instead of all the hospital in Washington. They realize that there's a link between the three administrators. Alec checks their credit card records and confirms that they were all in Berlin three years ago for a symposium on bio-terrorism. Udall gave the speech and they figure that he can help them if he's not dead already.
Vance and his team close in on the property. Senator Yount arrives and insists on overseeing the operation. Vance tells him that his warrant is on the way and Yount tells him to wait.
Parker, Eliot, and Alec go to Udall's home address and Alec goes in first. He realizes that he's stepped on a pressure plate and they spot a claymore mine on the floor ahead. Parker climbs up on Alec's shoulders then slides around his front, still holding on, and then bends backward and cuts the connection. They realize that Udall is Ahmed and finds records showing that Udall was fired from the CDC when he became obsessed with viral terrorism. Alec finds records showing that Udall has created a gas bomb that will function as a delivery system. Eliot realizes that everything is at the house and they wonder what is at the trailer.
Vance and his men close in on the trailer while Yount picks up Vance's phone. Eliot demands to talk to Vance but the senator hangs up on him. Alec takes the phone and hacks into Vance's Bluetooth speaker link. He then accesses the van's electrical system and uses the horn to send out an SOS in Morse code. Vance draws back from the door just in time and orders everyone back. The trailer explodes and Alec hacks the car speaker to confirm that Vance and his men got clear in time.
Parker checks the refrigerator and discovers that it's full of eggs. Eliot figures Udall will go somewhere with a lot of people and Alec starts tracking Udall's phone via the GPS. They place him in the subway and head down after him but there are too many people for Alec to pinpoint the signal.
Udall boards the subway car with a briefcase. As the car pulls out, Alec confirms that his signal is moving and he's on the train. Parker is already on the train and Alec and Eliot steal a car and drive to the main terminal. If Udall releases the virus it will spread throughout the city. A patrolman comes after the car and Eliot speeds up, while Parker heads for the booth to stop the train. She loses her grip and is blown back, but keeps crawling forward.
More police cars join the chase and Alec confirms that there is a maintenance tunnel at the next bend in the tunnel. He tells Parker to stop the train so that they can access it, and she climbs down the side and hits the emergency brakes. When the car stops, Udall activates the briefcase and stands up.
Alec and Eliot get to the maintenance tunnel entrance, enter through the door, and lock it behind them.
Parker enters the subway car and looks for Udall. Alec realizes that Udall used the eggs to culture a vaccine and he's immune, so he will be the only one who isn't panicking. Parker bumps into Udall and he reacts, and she realizes he's recently given himself the vaccine shot. Udall draws a gun and insists that the government has to learn that people will die. Eliot and Alec get everyone off the train as Udall rants that he plans to make the government wake up. He reaches for the case only to discover that Parker has stolen it. Eliot charges at Udall, who shoots him in the chest, and the hitter takes out Udall.
Alec examines the case and discovers that it has a glass cover that is wired to explode. However, Parker kept one of the diamonds from the earlier theft. She uses it to cut open the case and Alec goes to work. Meanwhile, Udall wakes up and crawls for the discarded gun. Alec disables the bomb but discovers that there's an aerosol spray that will put the virus into the nearby atmosphere, killing everyone in the city. Udall grabs the gun and shoots at them, and the trio takes cover.
Parker and Eliot exchange a look and then Eliot runs at Udall while Parker grabs the briefcase and runs down the tracks. Once she's clear, she applies the miniature blowtorch to the aerosol outlet as it release the virus, destroying the virus. Alec hugs her, telling Parker that he can't lose her.
Later, Vance tries to recruit the injured Eliot to serve with him full time. Eliot points out that Udall believed he was doing the right thing and became obsessed, and refuses to work with his former teammate. Vance asks if he'll consider it and Eliot says that he's working with Parker and Alec now.