NCIS's season 4 begins in uncertainty as the team recovers from the emotional turmoil caused by an injury Special Agent Gibbs sustained while on assignment. Gibbs, a former Marine gunnery sergeant whose skills as an investigator are unmatched, formerly led this troupe of colorful personalities.
When Ziva accidentally witnesses a political assassination, she must surrender to the FBI and deal with the consequences without Gibbs's help, who is now enjoying his retirement. She learns that the FBI is looking for her and escapes, while the NCIS team, led by Tony, must prove that Ziva is innocent. However, when things get more complicated, Ziva seeks help from the one person who always trusted her, Gibbs.
Gibbs is forced to come back out of his retirement to help Fornell, who is being threatened by a convict that escaped from prison. The convict threatens both Fornell and his daughter Emily. Gibbs and the NCIS team re-open the convict's old robbery case, and question a retired sailor who is the only one who contacted the convict after he was sent to prison. The investigation will lead the NCIS team to a surprising discovery.
An abandoned car is found full of blood, registered to a missing Navy lieutenant. The NCIS team learns that the missing lieutenant was profiling men, trying to find a perfect man for herself. When they find out that the woman intended to go to a seminar at a local hotel, Ziva goes undercover to find more information. Ducky is busy going through the profiles of the men. Jenny makes a secret offer to Tony.
After police pull over a driver and arrest him for a concealed weapon, a car crashes into their patrol car with a dead man behind the wheel. The arrested man turns out to be Russian and Homeland Security claim he was working for them. The Russian is linked to an old case that Mike Franks worked on. Mike comes out of retirement to put the Russian behind bars.
When a missing Lance Corporal is found dead in a vacant house, the NCIS team discovers that he was buried in the backyard and then exhumed. They learn about his identity and that he was to be deployed to Iraq, but he never showed up for duty. The investigation leads them to a new clue---he had two fiancées. Abby runs the DNA samples from the two women to find out if the DNA is a match to the soil found on the dead man's body.
It's Halloween and the NCIS team is busy investigating a ransom case. A Marine's daughter has been kidnapped after the kidnapper attacked a Marine in his home. The investigation leads them to a fact that the couple has been separated. They decide to focus on the wife's ex-boyfriend, after learning that the woman is the one who destroyed their marriage. Meanwhile, McGee and Tony are stunned by Abby's Halloween costume.
When a Marine Colonel dies in an explosion at a military golf course, the NCIS team must investigate a suspected terrorist attack with the help from the Army Criminal Investigative Division (CID). The CIA gives them a lead to an abandoned warehouse, but it turns out to be a trap---the warehouse is set to explode. McGee uses his computer skills to break into the secret government files to uncover the terrorist cell.
When an honored Marine veteran is found dead in a hotel, the NCIS team must find out what happened to him. Soon they realize that the Marine didn't commit suicide and that he was a homeless man. After going through his stuff, they find compromising evidence against him, and Gibbs is determined to prove the man's innocence.
McGee breaks the rules, risking his NCIS job, to help his sister Sarah, who shows up disoriented and bloodied. While he works on figuring out what happened to his sister, the NCIS team is investigating a case of a Navy sailor, who is somehow connected to McGee's sister. Both Tony and Abby are busy with love problems, while McGee turns out to have another secret.
When a burnt and mummified body of a missing and wanted person is found on a Marine base, in a furnace, NCIS must work with FBI. The burnt man turns out to be a serial killer. The both teams visit the man's family and discover something shocking. Also, the NCIS team must deal with the book McGee wrote about them, using "fictional" characters.
When an artificial intelligence scientist is found dead in the prototype of a self-guided Humvee she had been developing, it appears she simply committed suicide. But when Abby conducts her search of the vehicle back at the NCIS lab, she inadvertently triggers a trap that pulls the safety belt tight to restrain the passenger, as exhaust is pumped in to the car. Confident now that it was a murder, the team investigates who at the A.I. lab would have the motive to kill the victim. Their main suspect is Torsten Engler, a bitter colleague who felt the victim was overshadowing his work. But, when more evidence is discovered Gibbs and the team are forced to refocus on someone closer to the victim.
After an intelligence officer is found dead in a small town outside of Washington, the NCIS team rushes to the scene of the crime, only to discover that the crime had occurred three days earlier. Having to rely on the local police for the facts in the case, Gibbs is less then thrilled at the apparently spotty work performed by local law enforcement. They discover that their main suspect is an Iraqi working as in informant for the US and that our victim was the one who helped him set up a new identity in the states. In the end Gibbs and his team discover a web of corruption and cover-up much higher up the food chain.
After 10 kilos of highly toxic chemical weapons go missing, Gibbs and his team scramble to find it. The chemicals had appeared to have been skimmed off the top of a delivery to a research company by the delivering officer, and had been sold to Mamoun Sharif, a violent and unpredictable terrorist. However, the team quickly discovers that one of the research company’s employees had attempted to anonymously sell a modified and harmless version of the chemicals in an attempt to scare the public and to make the company’s stock price go up. But Sharif had discovered a way to make the chemicals active again, and had hatched a plan to unleash them on all of the major cities in the north east. With time running out, the team must find the chemicals and stop the terrorist.
When the NCIS team captures Goliath, an international arms dealer, they discover that the Navy’s top secret "ARES" weapons system is about to go on sale to the highest bidder.
When a young Navy sailor is discovered dead in an abandoned restaurant, what appears to be death by a drug overdose turns out to be a poisoning.
When a Navy Lieutenant becomes the victim of radiation poisoning, the NCIS team must find the person who's behind the crime. The Lieutenant, who is working for the IAEA (International Atomic Energy Agency), claims that only his two colleagues knew about his assignment, and whoever it was, the person tried to stop the Lieutenant's next investigation.
Gibbs investigates an explosion of mutilated human remains at a mausoleum at a national cemetery. However, the remains didn't belong to any of the crypts.
When a supposedly frozen to death Marine turns out alive on Ducky's autopsy table, the NCIS team has to find out about the victim's movements last few days to uncover what happened to him and who left him for dead. As the investigation progresses, the team learns about the victim's trip to Baghdad via a private cargo plane and discovers a link to Gibbs' past.
When a weekend call to the NCIS tip line from an unknown source about possible terrorist activity results in the death of two agents sent into a trap, the NCIS team will have to find out who were the people responsible with the help from Agent Paula Cassidy, who holds herself responsible for the tragedy.
McGee is under high pressure during the murder investigation of a Petty Officer based on the character for his latest book, with very little information to go on.
Still on the trail of Le Grenouille, Director Shepard attempts to meet with an informant who is willing to give up valuable information about his organization.
After a blind photographer discovers that he'd photographed a dead man deserted in an alley, the blind man’s memory and photographs of the scene become NCIS's only leads in the case. Using these tools, the team is able to trace the murder back to a co-worker of the victim, who himself was under investigation for embezzling funds. But after the co-worker is found dead with a suicide note confessing that he and the victim had been running an embezzlement con, and that he'd murdered the victim when they had a falling out, Gibbs' gut tells him the note was coerced. Gibb's skepticism is proven correct after a particularly astute observation by the blind photographer, and a cryptic message left in the suicide note, lead to the true killer.
When Jenny has to attend an overseas conference, Gibbs is made acting director, but he prefers to ignore his duties and lead the investigation of the murder of a man, who was found dead in a taxi headed to the NCIS headquarters.
Armed with new information from a Russian officer about her deceased father, Director Shepard returns home from an international conference to discover someone has broken in to her private study. She takes heed of the Russian's insistence that her father was not the upstanding officer he appeared to be, and that he was still alive, as she notes the items that are out of place, items that her "dead" father was familiar with. She turns to Gibbs' team for help investigating, frustrating them by offering little explanation as to why they are investigating. Meanwhile, Tony and his doctor girlfriend, Jeanne, have an extended confrontation with a junkie prostitute and her pimp, after the junkie's brother dies from a drug overdose resulting from serving as a "drug mule."