Having successfully recovered from his near-fatal shooting at the end of the pilot episode, "Legend", Callen rejoins the OSP team whose headquarters have since moved to a new location. His first case back involves a Navy commander who was kidnapped by a drug cartel and eventually killed in a shootout between the cartel and members of the LAPD. The team soon discovers that the commander's actions might have jeopardized a highly classified military operation against various drug cartels in Mexico and also put the life of his young niece in great danger, forcing the team to race against the clock to find and save the young girl before it's too late but all is not what it seems.

Guest starring: Mathew St. Patrick, Clare Carey, Alex Fernandez, Ariel Gade

Sam is left feeling betrayed when he learns that a military-style hit on a drug dealer was carried out by a group of former SEALs, people that Sam himself trained, but the double-crossing might run much deeper than originally thought and might even involve a member of the LAPD.

Guest starring: Rodney Rowland, Matt Battaglia, Brian Gross, Seidy Lopez, Whitney Anderson

Note: The episode title is stated as being a motto of the SEALs. "The Only Easy Day Was Yesterday"

During a Marine Corps training exercise, an MQ-1 Predator and Hellfire missile are hijacked and stolen leaving a Marine dead. The team is forced to step into the hacker underworld in order to get answers and also retrieve the missiles before they fall into enemy hands, thereby putting the entire country at risk from a rogue missile attack.

Guest starring: Warren Kole, Andrew Borba, Christian Kieber, Brian Kubach

A mentally unstable Iraq war veteran arrives in L.A. and his actions trigger a series of killings. As the team looks for the former Marine, a private security firm with its own deadly agenda muscles in, threatening the case.

Guest starring: Jeanette Brox, Jonathan Adams, Chris Tardio, Rob Evors, Jay Malone, Fay Wolf

A defense contractor is murdered while on a jet-ski, and the team fears that his classified-software secrets are lost until they find a suspect: a North Korean assassin named Lee Wuan Kai, who has possible connections to Director Vance and whose own presence has also haunted Vance for several years. Meanwhile, rookie Agent Dominic Vail goes on an undercover assignment for the first time. This is continued in the NCIS Season 7, episode, "Endgame".

Guest starring: Kelly Hu, Kelvin Yu, Kathleen Munroe, Michael Marisi Ornstein

A Marine corporal is found dead after dropping from the top of a high rise apartment building. The LAPD think it to be suicide, but NCIS is brought in and soon figure out that he was murdered. As they investigate the death, a major counterfeiting ring is uncovered and a Secret Service agent arrives to help them with the case despite the team's best efforts to brush her off.

Guest starring: Monet Mazur, Gregory Scott Cummins, Mark Rolston, Brandon Scott, Rachael Carpani, Tyler Jacob Moore, Burnadean Jones

A range of surveillance photos found on the body of a murdered woman has the team tackling the cold case of Callen's near-fatal shooting several months ago. They eventually set up a very dangerous assignment: to find out who ordered for Callen to be killed and to also bring his would-be murderer to justice.

Guest starring: Charles Esten, Andrew Rothenberg, Gregory Sims

While Hetty is attending a Senate hearing in D.C., the investigation of a murdered Marine Lance Corporal leads the NCIS team to stolen anti-tank missiles and a dangerous militia group which Special Agent Mike Renko has been investigating and as such, both Callen and Sam are caught in the middle.

Guest starring: Michael Reilly Burke, Brian Letscher, Owen Beckman, Richard Brake

When a Navy engineer is murdered, the team believe that international espionage might be the motive for his death but they're in for a shock when Forensic Scientist Abby Sciuto (Pauley Perrette, reprising her role in the original NCIS) arrives in from the Navy Yard in Washington D.C, having traveled to Los Angeles with information suggesting that a possible serial killer, one she calls the Phantom is responsible. She also claims that what makes him so unique is his M.O. which is that his killings are totally random with no repeats and that the killer himself also leaves no physical evidence of any kind behind. However, when Abby herself is kidnapped after spending the evening at a bar with Eric, Callen and the team find themselves racing against the clock to save Abby's life and stop the murderer before it's too late.

Guest starring: Kris Lemche, Sean Wing, Dawn Stern, Tanya Clarke, Adrian LaTourelle

A trio of Marine veterans are targeted by a bomber with one of them dying as a result of his cell-phone exploding and the evidence leads the team to a disfigured ex-serviceman who's been fingered for murder in Iraq.

Guest starring: Rich McDonald, Assaf Cohen, John Siciliano, Patrick Pankhurst, Caitlin Keats

When a petty officer is murdered, the team discover a plot at a strip club that involves intelligence secrets which are being extorted and presumably sold. Meanwhile, a vulnerable young friend of Sam's is unknowingly recruited by an Islamic militant.

Guest starring: Henri Lubatti, Jana Kolesárová, JR Bourne, Ronald Auguste, Josh Kelly

One of Callen's old aliases is brought back to life as he prepares to investigate the shooting of a sailor and in the process, he uncovers a shocking secret from his past.

Guest starring: Jeffrey Pierce, Kenny Johnson, Audrey Marie Anderson, Michael Irby, David Monahan

Hetty receives an "Agent needs assistance" call from Special Agent Dom Vail. The NCIS team find his blood covered car, but soon become convinced that the blood is not his, leaving the team wondering if Dom is dead or alive. The episode ends with the team struggling to come to terms with Dom's disappearance while Callen files a missing persons report for Dom, officially classifying his status as "Missing".

Guest starring: Onahoua Rodriguez, Maurice Compte, Parry Shen, Gonzalo Menendez

The agents discover that a biochemical weapons expert suffering from Alzheimer's disease was tricked into producing a deadly toxin for an arms dealer. When Sam goes undercover to the auction they learn that there will be a demonstration of the weapon in a Los Angeles mall, and the team must hurry to stop it.

Guest starring: Julianna McCarthy, Andrew Connolly, JR Bourne, Dameon Clarke, Burt Bulos

While attempting to open a security deposit box at a bank, armed robbers hold hostage and then start battling with Special Agent Kensi Blye, leading to her being shot in the chest. The events of the day before are then revisited, revealing that Kensi's injuries are not as they seem and neither are the robbers.

Guest starring: Devon Sawa, Brian Goodman, Mac Brandt, Scott Alan Smith, Ian Harding

The team suspects that the death of a naval officer ruled as a suicide could be a murder, and that the crime implies a possible threat to national security. And things get worse when it's discovered that the victim was actually a spy working for the Chinese government with technology capable of compromising an important mission he was due to embark on before his suicide. This revelation leads the team to a rogue sleeper cell and they must save the victim's family before it's too late.

Guest starring: Tzi Ma, Elizabeth Sung, Angela Oh, James Harvey Ward

The team investigates the death of a sailor who died in an underground street race, and they find that his car was sabotaged, resulting in it later exploding, killing the sailor. Meanwhile, having been caught speeding again, Callen, on Hetty's orders and much to his own dismay, is forced to go to traffic school while the rest of the team handle the case.

Guest starring: Dichen Lachman, Scout Taylor-Compton, Jake McLaughlin, Walter Perez, Lew Temple, David Andriole, Helena Mattsson

A Marine is killed in a gang-related drive-by shooting, and the team fears his younger brother may also be targeted. They soon uncover evidence of an operation smuggling automatic weapons which are being taken from the Iraqi battlefields and placed into the hands of a local street gang.

Guest starring: Sticky Fingaz, John Lafayette, Paul James, VJ Foster

The investigation of an ex-marine's murder leads the team to a mixed martial arts gym, where Sam must go undercover. The team soon realize they've stumbled into an LAPD Case, and meet LAPD Detective Marty Deeks while he's undercover. The investigation becomes a joint operation.

Guest starring: Matt Gerald, Graham Hamilton, Dayo Ade, Winston Story

Recruited by Hetty, Detective Marty Deeks officially joins the team as the NCIS/LAPD liaison officer. The death of a marine leads the team to Hollywood glitz and glamor in search of a young girl who may or may not be responsible for the marine's death and a series of high-society home invasions. At the end of the episode, Deeks leaves to go undercover on an LAPD op but promises to return.

Guest starring: Bernard White, Faran Tahir, Cherilyn Wilson, Brook Kerr, Nick Jandl, Mandell Butler

After months of getting nowhere, the team finally receives video evidence of Dom being held hostage several months after his original kidnapping in "Missing". With a deadline being issued by the group who also demand the release of its captured leader, the OSP team rushes to Dom's aid in hopes of saving him before the deadline expires but the final outcome might be something no-one was expecting and when it does happen, the team finds itself being forever changed as a result.

Guest starring: Daniel Hugh Kelly, Carlo Rota, Ben Youcef, Abdoulaye N'Gom

The team searches for the head of the terrorist organization responsible for Dom Vail's kidnapping and who escaped from Army custody during a secretive transfer. Meanwhile the OSP team struggle to come to terms with Dom's tragic death and Hetty has second thoughts about continuing on as OSP's Operational Manager.

Guest starring: Yancey Arias, April Parker Jones

Callen's cover is blown and at the same time the NCIS OSP's computers are hacked, forcing the team to go off the grid for the time being. The team struggles to get back on its feet while at the same time investigating the source of the security breach which is later revealed to have come from a shadowy intelligence dealer who has ties to an Eastern European mafia group.

Guest starring: Peter Wingfield, Steve Bacic, Gregory Alan Williams

The NCIS team races against the clock to stop a brutal and murderous cabal who are hellbent on launching nuclear war in the Middle East while Callen finds himself embarking on a very personal and possibly the most dangerous mission of his entire career so far- to find the woman who might hold the answers to his true identity and past.

Guest starring: David Dayan Fisher, Eli Danker, Nancy Linehan Charles, Jacqueline McKenzie