A group of gunmen wearing masks attacks a Department of Defense office during lunch. One man, Milton Mulrooney, survives and runs to Mexico. Sam and Callen follow him on an unsanctioned mission. They run into DEA, who swap out their weapons and vehicle keeping NCIS supplies for themselves.
NCIS loses contact with Sam and Callen. Meanwhile, Deeks and Kensi investigate the scene of the crime.Several servers went missing that contained the budgets for covert operations. Doug would have been there for the shooting, but he forgot his lunch.
Sam and Callen head to a brothel to get information about Milton. The prostitute that Milton visited gives them a location for him. They take her with them because a group of suspicious men show up. The men pursue Sam, Callen and the girl with guns blazing. A firefight breaks out on the street. Callen gets the car, but it gets shot up so they steal a taxi to escape.
Sam and Callen find Milton. He was hiding out with a family in Mexico. One of the daughters believes he's going to marry her and take her family to America. Milton believes it's the US government who is trying to kill him. The mother pulls a gun on Sam and Callen.
Deeks and Kensi find the killers' burned out vehicle. They find the servers inside the car. They believe the men weren't trying to steal the information, but wanted it destroyed.
Milton and his co-worker, Margaret, found monies were being allocated to Delta black ops code named, "Duster." The operation was never sanctioned by the government. Someone robbed the government of $40 million and they told their boss, Doug. Everyone knew that both the employees always brought their lunch. Milton believes the Delta unit targeted them.
The Delta team show up and demand to discuss terms. They took out the cell towers so Sam and Callen have no way to contact help.
Eric wasn't able to recover information from the burned drives. He worked with Nell to search the file back-ups for the authors of the files. They found two budgets for "Duster," but each was reporting to different committees. It appears the Delta team stole the money and killed the people.
The Delta team wants Milton and say they will let everyone else live in the house. The Delta team has high power weapons, while Sam and Callen have handguns. Army General Keys says he doesn't know where the "Duster" group is. They are given an objective not a mission. Keys says he will try to find them. Granger goes to Mexico to find Sam and Callen.
Kensi and Deeks bring Doug in for questioning. He has $3 million in a Swiss bank account. He denies knowing about the money. Nell finds that the ID used to open the account didn't have Doug's photo on it, instead it was the picture of one of the Delta team members.
Kensi and Deeks figure out that Milton was in on the scam. The gun shots in the bathroom missed him on purpose. The team wanted to kill Doug, but he forgot his lunch.
The woman shows Callen money that Milton gave them. Sam and Callen realize Milton was in on it. The mother hits Milton and he's tied up. The Delta guy tells them to give up or they will attack.
Callen tries to get the Delta guys to hold off their attack because they need Milton. It doesn't work. They fire on the house and then NCIS and the women fight back with supplies they have available. Sam and Callen count down the few bullets they have left to fight back and waste them.
Sam holds Milton hostage to negotiate the women's freedom. He assumes they are out of ammo and comes into the room. Someone else arrives and shoots them. It's Granger. The Delta guys are all dead. Granger brought the real "Duster" team to take out the fake team.
Sam and Callen left some of Milton's money behind for the women. Granger agrees with the money in the bag is all there was.