At a naval base in Bahrain, a man enters a room and opens a safe. As he places a flash drive and a gun inside he is attacked by someone wearing all black. The attacker beheads the man and takes the flash drive.
Hanna and Callen are shocked when they find Deeks working when they arrive at headquarters. They ask Kensi why he might be so tired but she has nothing to say. Callen points out that she's wearing the same shirt she had on yesterday. Eric calls them in for debriefing while Hetty watches them all from above. She tells Granger that the price has gone up but he says something else has come up. He hands her a file and says she won't like it. The folder is about a classified project White Ghost. She says it was only a matter of time.
Nell explains to the team how Hill was murdered right before he was set to deliver a plan on how to seize Pakistan's nuclear arsenal. The team worries that this information could be used for nefarious purposes. Callen has been to the base and says it's secured by warriors known as Gurkhas. The knife used to murder Hill was a knife that belongs to Gurkhas. The flash drive is now being tracked to a hotel in Hollywood.
Hanna and Callen enter the hotel and approach a room. Deeks and Kensi enter the room next door because it's not sure which room the flash drive is in. A man shoots at Kensi from the parking lot and the team moves to take him down. Callen shoots a man in the hallway but he doesn't have the flash drive. Kensi finds a scared little girl and tries to comfort her. A man holds his gun to Kensi and orders her to drop her weapons. The man lets the girl girl and Deeks moves towards them. Kensi orders him to take the shot but he refuses. A car pulls up and the man gets in. Kensi picks her weapons up and punches Deeks in the face for not taking the shot.
The team returns to headquarters and Eric tells them the GPS signal has been disabled. Nell states that the man who was shot was from Pakistan. Callen thinks that Pakistan tried to frame India for the murder of Hill. There are still two Pakistani agents on the loose with the flash drive so Callen tells Eric to find them.
Hanna and Callen explains to Hetty what happened at the hotel. She asks if their team is ready and Callen says he hopes so. Hetty doesn't think hope is an option.
Deeks confronts Kensi in the shooting range. She points out that he would have taken the shot 24 hours ago. He agrees that he would of but it's not yesterday anymore. Eric walks in on their conversation and says the LAPD found the body of one of the shooters from the hotel.
At the scene of the crime they discover that the dead shooter doesn't have the flash drive and he was killed with one cut. Callen suspects that the shooters were ambushed by Gurkhas who didn't like being framed. Hanna thinks the killer is closer than they think and he looks over at a man that matches the physical description of a Gurkha. As they walk over the man runs away. They chase after him and he pulls a knife in an alley. Hanna and Callen fight with him and manage to knock his knife away. He doesn't have the flash drive and admits to being a Gurkha. He shouts something out and Hanna says that it's their war cry and the Gurkhas are coming.
Callen and Hanna question the Gurkha, Jemadar Thapa. He admits that India's minister of Defense sent him to clear the Gurkha name. Thapa says he is only here to carry out his orders, no more and no less. Callen suggests that Thapa actually has the flash drive.
Hetty says the White Ghost is a dangerous man and it will be a dangerous mission. That's why Granger will handle it himself.
Nell thinks that the remaining shooter will try to take a private plane out of the country. She searches for the car in parking lots near airports and finds a match. Hetty enters and asks her to get Callen.
Callen gets off the phone with Hetty and tells the team that they are to take Thapa with them. SecNav has ordered them to treat him as a member of the team. Deeks takes Thapa's handcuffs off and welcomes him to the team. He tells Thapa that he trusts him and the two become friends. Thapa promises not to let him down.
Callen, Hanna and Kensi head to the airport in search of the remaining shooter. Kensi prepares a sniper rifle and refuses to talk about her personal life. Callen spots the man and tells Deeks to move in when he sees the flash drive. Deeks sneaks around a building with Thapa to get a better view. The man exchanges money with a pilot but then shoots him. Callen tells Deeks to move in but Thapa is already gone. The man fires at Deeks when he tries to stop him. Callen and Hanna move in behind Deeks and they search for the man and Thapa. They find the man dead but no sign of Thapa. The flash drive is gone.
Hanna reminds Deeks that he's not in this alone. Thapa is loose and now the most wanted man in LA. Deeks regrets not taking the shot that would have stopped the man so Callen suggests that he get them back in the game. Deeks thinks he knows a way to get Thapa and the flash drive back.
Deeks tells Hetty that he can make it right. He doesn't think Thapa will sell the flash drive but will instead bring it back to India. The only way to get a fake passport is from a gangster that Deeks had mentioned to him. He once went undercover as a lawyer to try and bust Talita Pambakian. She found out another officer was undercover and shot him in the head. Deeks wants to reestablish contact and beat Thapa to her.
Kensi doesn't like the mission because there is no way to contact Deeks if something goes wrong. He wants to pretend they are just two ordinary people and he asks her to dinner. He can't take a gun with him undercover but she offers him her knife.
Deeks enters Talita's storefront posed as Marty Finch, a lawyer. The NCIS team listens from outside but the signal is weak because the walls are made of thick concrete. Deeks hides the knife as the security guards pat him down. He meets with Talita and says that an undercover cop is coming for her. He describes Thapa and offers to work for a percentage rather than a fee this time. She says he must earn his pay and has her guards escort him to the freezer in the next room.
In the freezer, Thapa is tied up by his hands. Talita asks Deeks to prove his loyalty and hands him a gun. He takes the gun but says he doesn't shoot people. Talita informs him that it's only loaded with one bullet and if he doesn't shoot Thapa he will also be hanging there. Deeks raises the weapon.
The team outside loses contact with Deeks when he enters the freezer. Kensi gets out of the car and rushes the building. She takes out the security guards outside and heads in as Hanna and Callen cover her. Kensi rushes in but Talita shoots Thapa. Deeks takes Talita out and carries Thapa out of the freezer. Hanna finds the flash drive in Talita's coat pocket.
Kensi meets with Deeks outside. She says they will figure things out and talk about their situation. She promises to talk if he promises to be patient with her. Deeks leaves in the ambulance with Thapa. On the way to the hospital, Thapa tells him that he will never forget what he did for him. Thapa advises that Deeks take his time with Kensi and she will wait for him.
While waiting for Deeks at the headquarters, Granger tells her to pack her things. There's a plane waiting for her because she has been reassigned. She asks Hetty if it's true and learns she will be back when the job is done. Hanna asks Hetty what it's about but she can't say.
Deeks returns to find Kensi gone. Hetty informs him of the classified mission she is taking part in. He asks how long she will be gone and Hetty says indefinitely.