The field team travels to the Romanian Black Sea coast, where Callen recognizes his childhood roots. They hoped to find and rescue Hetty by surprise, but are awaited by the hostile gypsy crime gang Comescu. Eric and Nell juggle obeying the Director, who takes over while Hunter is also to Romania, and informing the team after illegally accessing Hetty's actual Comescu file.
Dennis Calder, whose software was used for a cyber attack against the Department of Defense, has been kidnapped and his driver shot. The team fears an attack on his family, but finds wife Heather Marcum is resigned to a marriage on paper while bright teenage son Shawn misses his daddy terribly. Nick, an ex-cop, may have dragged Dennis into a drug deal. Callen won't accept Hatty's replacement, let alone his past remaining a closed book, while Eric and Nell adjust painstakingly to the new supervisor. More hacking cracks the case surprisingly.
Special Agent Sam Hanna is sent undercover as a bomb specialist as the team races to locate stolen explosives somewhere in the city. Meanwhile, to much protest, Hunter changes the dynamics of the team and has Callen partnered with Kensi and Sam with Deeks.
Cameraman Steve Downey sees his TV-partner, reporter Adriana Gomez, shot on Venice Beach. After their main informer, Navy expert on Lybia commander Gavin Madison, is nearly shot at home, it's clear the fiends must be from that country. The trail leads to Asad Al-Libi, the elusive masked anchor of a clandestine anti-Khadafi TV station, but who, where and why prove surprisingly complicated. Meanwhile, Deeeks's canine buddy Monty earns team mascot status and Callen learns everything Hetty claims to know about his CIA family antecedents.
The LAPD officially asks NCIS for help after one of three thugs shot in a raid on the Mexican Molina drug cartel is identified as a member of Jamel Ahmed Shallah's Al-Qaida branch. The investigation for the link between both illegal organizations is gravely complicated by apparently fake FBI agents, who 'clean up' everywhere just before the team arrives, and by Mexican police commissioner Eva Espinoza, who is on a personal revenge quest but has an informer and bonds with Deekes. Meanwhile the whiz duo searches behind Hetty's back for Sam's stolen heirloom classic car.
After a murder on a retired US Navy intelligence officer, her husband Cliff is puzzled, but the team soon discovers all she told him about her professional life was a cover. She worked as an analyst for a water company, which doesn't explain either why she had secret contacts concerning Afghanistan. Hetty knows the man, traumatized former top NSA-agent Larry Basser.
When a dishonorably discharged Marine kills a Japanese tourist, the team tracks him down. He claims that while in Japan he fell in love with the daughter of powerful and wealthy Japanese man. It seems the man didn't approve of their relationship and framed him for a crime which led to his discharge. But the daughter knows he is innocent. She left Japan with him and she is in hiding. When Callen and Sam go to talk to her she's gone. They learn that her father got her and is planning to bring her back to Japan. So the team has to find a way to rescue her without letting...
NCIS is charged with investigating the killing near the Mexican border of soldiers Paul Green and Brandon Chase, who smuggled a heavy, missing box. It appears to have contained gold from Qatar or drugs, as their killers belonged to a Mexican heroin cartel. Ultimately it turns out to be a nightmare in its own, enough uranium for a dirty bomb or other nuclear terrorism, ordered by Al Qaida-affiliates, as investigated in Sudan by CIA agent Michael Saleh, Sam's secret other job. But what's the L.A. target, about to be hit hard?
The CIA reports several casualties in Khartum, including an unidentified one matching Sam's physique. Callen flies to Khartum, where Sam, still alive, is dating the daughter of an Al-Qaeda-affiliated Islamic fundamentalist governor in the rebellious south, while employed for regular security checks. The LA team meanwhile races against time as a mole in the CIA operation may fatally expose Sam.
During an NCIS-assisted, LAPD set-up operation to arrest an arms dealer, Dekes fatally shoots an aggressive suspect whom he wrongly assumed to be armed. Dekes is suspended by the LAPD, and hence as NCIS liaison. the prospect of a final separation brings Kensi to admit she really cares for him.
The NCIS team must locate a classified device with the power to destroy Los Angeles that was stolen from a college research facility. Meanwhile, Sam tries to track down a highly sought-after Christmas present for his daughter, and Eric meets Nell's parents.
When a vehicle transporting Jada Khaled is ambushed, NCIS must track down the culprit to save her and their case. Meanwhile, Sam is forced to confront Jada for the first time since returning from Sudan.
Interpol's Stockholm agent Martin Källström enlists NCIS's help after the murder of two businessman in the MO of a chameleon-like serial killer associated with a French-Maroccon illegal arms gang. Assistant director Owen Granger criticizes Callen for letting him escape, but at great peril the team shows the deception is far more devious and complicated. Callen is targeted for personal motives.
Assistant Director Owen Granger takes Kensi in 'protective custody' because she was the last person known to have contact with a secret elite snipers unit her late father belonged to. Granger doubts her loyalty, postulating she joined to be able to take revenge for his death on the unit, which recently lost several snipers. The boys are determined to find the real killer. They withhold evidence against her as long as possible and look into a CIA connection. A secret file is hoped to provide crucial clues.
NCIS Assistant Director Owen Granger seems the link between the recent killings of the team Kensi's father was part of, but explains he has to eliminate as suspect to be sure about the only alternative, Peter Clairmont, who masterly staged his own death. Deeks learns why Kensi seems obsessed by a certain Megan Stevens, whom he agrees to guard for her, yet she's the one shattered by the truth concerning her father.
The Navy secretary is invited to an Asian conference in the L.A. Vietnamese consulate, which recently suffered attempted arson. Poor tailor Tuan Nguyen is shot from a driving car while trying to enter. He's to scared to tel why he carries the name of Vietnam veteran James Cleary, a tour guide and retired social worker. His employers, Binh and yen Tran, run a ruthless sweetshop. Nearby the car of Cadeo Hoang, a lawyer and leader of a movement for democracy in Vietnam, is bomb-wrecked, according to him to discredit the movement like its violent precursor. A computer ...
Navy SEAL petty officer Third Class Doug Foster's corpse is found on a base practice course, probably meant to have the fatal blows covered up by artillery practice. His team must leave within hours for an Afghanistan Taliban-held hostages rescue mission they alone can carry out after elaborate training. They probably know but cover up the truth, yet won't talk to 'outsiders' like NCIS, at best to SEAL-veteran Sam.
NCIS feels passed-over when the FBI arrests honorably discharged Afghanistan veteran Gavin Knowles after finding a chemical bomb in his car. Psychologist Nate Getz helps questioning FBI Special Agent Jonas Ambrose's terrorism story, which is discredited when a worse bomb is found. The team soon finds Gavin's house-mate Mia Jameson leads a double life with Adam Malnick, and carries a more personal grudge.
Deeks and Kensi pose as a married couple to observe a closed block where a Russian 'sleeper' spy is believed to live but their informer is murdered. They enjoy it beyond the usual banter, growing closer despite some mishaps. Each suspect neighbor requires a different approach, from senior recluse Floyd Hobbs to gay couple Rob and Bob and the libertine Boltons. Callen's contact Arkady Kolcheck lies about knowing 'neither', and is attacked on the Russian handler's orders, as is the neighbor who comes clean when cornered.
The Mayfield family's federally licensed weapons store with private gun range is suspected of illegal arms sales. After its patriarch is shot, the team is ordered to warn off and help retreat NCIS Special Agent Mike Renko, who was undercover there on a mystery undercover mission. After a sniper shoos him surprisingly, assistant director Owen Granger reveals he was his handler, absent on a DV mission. Kensi sits at Renko's sickbed, but he dies after surgery. Meanwhile the boys, helped under coercion by Mayfield inside snitch Mara White, eliminate several hypotheses, ...
Having blown up NCIS special agent Lauren Hunter before their eyes, the Chameleon stuns the time again by announcing they'll be escorting him out of custody in a matter of hours. An apparent clue only leads them to a bomb that nearly kills them and seduces them to illegally arrest-blackmail Israeli 'consular officials'. Assistant director Owen Granger's present priority case, the kidnapping of Kevin Atley, who has the identity of the only agent who might be able to counter the Iranian nuclear threat, proves key to the Chameleon's plan. His demand however goes wrong ...