Originally broadcast between September 28, 2004 and May 24, 2005, the second season shifts away from the naval setting of the show somewhat, and includes more character development than the first season. Season 2 sees Norfolk Case Agent Timothy McGee promoted to full-time field agent, and transferring to NCIS HQ in Washington to work with the Major Case Response Team. This season also sees Ducky finally solving the meat puzzle he had been working on since Season 1. Caitlin Todd is shot and killed by Ari Haswari
| Series # | Season # | Title | Original airdate |
| 24 | 2x01 | "See No Evil" | September 28, 2004 (2004-09-28) |
| When an eight-year old blind girl and her mother are kidnapped to blackmail a Navy captain to transfer $2 million in government funds, Gibbs and his team are faced with a unique challenge. An unexpected twist is uncovered when Abby and McGee manage to trace the money. A delighted McGee becomes a permanent member of the team. |
| 25 | 2x02 | "The Good Wives Club" | October 5, 2004 (2004-10-05) |
| The mummified remains of a woman are found in an abandoned Marine home. The team discovers that the woman was missing for several months, was wearing a wedding dress when she died, and may have been a victim of a serial killer. The search for the murderer uncovers a similar case in Florida, and upon arrival, they start looking for connections between the women and the locations. Some clever forensics work from Abby, combined with profiling from Todd and Gibbs, reveals an unlikely suspect. |
| 26 | 2x03 | "Vanished" | October 12, 2004 (2004-10-12) |
| A marine attack helicopter is discovered in the middle of a crop circle in a rural area and the pilots are missing. Soon, NCIS discovers that only one of the pilots was on the flight, that there is a decade long feud going on in town, and that the missing pilot is out for revenge. |
| 27 | 2x04 | "Lt. Jane Doe" | October 19, 2004 (2004-10-19) |
| A body of a woman in a Navy uniform is found by two sailors on leave. Ducky links the murder to an unsolved case 10 years ago, and starts behaving strangely. He later reveals to Gibbs that the old case is the only one he has ever dealt with in which he did not identify the victim. When a note is found at the new crime scene, the handwriting is matched to a similar one left at the other crime scene. McGee's dedicated detective work, combined with Abby's forensics, puts forward a suspect. |
| 28 | 2x05 | "The Bone Yard" | October 26, 2004 (2004-10-26) |
| The NCIS team attends a crime scene, and end up finding multiple remains. When one set of remains is revealed to be an undercover FBI agent, the team realises that they have stumbled upon a dumping ground where the mob dispose of their victims. The FBI suspect an agency mole is responsible for the exposure and subsequent death of the murdered agent, and it appears as though Fornell is being set up to take the blame. Gibbs sets out to find the real mole and clear Fornell, using tactics that shock his team. |
| 29 | 2x06 | "Terminal Leave" | November 16, 2004 (2004-11-16) |
| When an Iraq veteran is threatened and very nearly killed by a group of terrorists, the NCIS team steps in to protect her and her family. While trying to convince an FBI agent to help them, the team is convinced that they've discovered the bomber. However, things might not be what they seem when another car bomb nearly kills Tony and Todd during their protection duty of the Lieutenant Commander. A family secret may pose more of a threat than even terrorists could. |
| 30 | 2x07 | "Call of Silence" | November 23, 2004 (2004-11-23) |
| A former Marine, and Medal of Honor recipient who fought in World War II, confesses to having murdered his friend in battle. Gibbs does not believe this is the whole truth and goes on to prove his innocence. The team become personally involved with the case, with Gibbs using deceptive tactics to pull the truth from the elderly man. |
| 31 | 2x08 | "Heart Break" | November 30, 2004 (2004-11-30) |
| A Navy Commander dies after a successful surgery. At first glance, it appears that the sudden death might have been a case of spontaneous human combustion. While researching the dead man's past, the team discovers that he had gained a lot of enemies recently, not least of all a young ensign, who makes himself the prime suspect with some bizarre behaviour. However, while analysing the evidence from the scene of the death, Abby and Tony discover the truth, and in turn find a new suspect. Ducky develops a soft spot for the doctor who was treating the commander. |
| 32 | 2x09 | "Forced Entry" | December 7, 2004 (2004-12-07) |
| A Marine's wife shoots an intruder in self defense when he is about to rape her. At first the teams believes that man got what he deserved, but the theory changes when it is revealed that the wife had been leading a double life (while her husband was serving overseas). Upon speaking to the intruder's sister, the team further theorise that the whole incident may have been set up as a 'date' by the wife, who got cold feet at the last minute. However, when Abby matches the intruder's DNA to a sample already held on file, the entire investigation changes. |
| 33 | 2x10 | "Chained" | December 14, 2004 (2004-12-14) |
| Tony goes undercover as an escaped prisoner. He is tasked with sticking to a convict who has information about stolen Iraqi antiques. During the investigation, Tony disappears, and the GPS locator that Abby placed on him is no longer working. After some startling discoveries in the case, the team realise that Tony's life may be in danger and must race against time to find him. |
| 34 | 2x11 | "Black Water" | January 11, 2005 (2005-01-11) |
| A Navy officer's body is found in a car pulled from a lake by a celebrity private investigator. The man had been missing for two years. The PI now wants to claim the reward posted by the family, but the NCIS team must complete the investigation to find the killer before the money is awarded. The case changes from accidental death to suspected murder when a bullet is discovered lodged in the car. The team initially suspect that the dead man's brother may be a prime suspect, but forensic evidence suggests someone unexpected. |
| 35 | 2x12 | "Doppelgänger" | January 18, 2005 (2005-01-18) |
| A telemarketer hears a murder while trying to sell a long distance call package. The team investigates with a civilian law enforcement team that seem strangely familiar. Each team member discovers different crucial facts about the case, leading to the discovery that the murder may not have been all it seemed to be. When Abby and McGee discover that the dead man was using the Navy computer system for his own financial gain, they consult with the people he worked with to see if they can shed light on who may have wanted him dead. |
| 36 | 2x13 | "The Meat Puzzle" | February 8, 2005 (2005-02-08) |
| Ducky and Jimmy finally begin to identify the bodies in the meat puzzle they have been working on for several months. It isn't long before Ducky realises he testified in a court case that the dead men were involved in, and it dawns on him that he might be the next victim. Tony and Todd are assigned to protect Ducky and his elderly mother, but a mistake by Todd leads to Ducky being kidnapped from his home. The team must race against time to find him before he becomes another victim. Jimmy and Abby work together to uncover the truth. |
| 37 | 2x14 | "Witness" | February 15, 2005 (2005-02-15) |
| A beautiful young MIT graduate (Danica McKellar) witnesses a sailor being strangled. Local police doubt her story, but McGee asserts that her account warrants further investigation. When a sailor's body is found at another location, the story gains ground. The witness also captivates McGee who, after a sudden twist in the investigation, unknowingly holds the key to solving the case. |
| 38 | 2x15 | "Caught on Tape" | February 22, 2005 (2005-02-22) |
| A Marine falls off a cliff, and his camera records him falling. The prime suspects are his wife and his best friend with whom he was staying in the camp. Gibbs finds out they had an affair behind a dead man's back and he tries to persuade them to blame each other. In the meantime, Abby reconstructs the damaged film footage on the camera and reveals a previously dismissed suspect to have been in the vicinity at the time of the death. |
| 39 | 2x16 | "Pop Life" | March 1, 2005 (2005-03-01) |
| A dance club bartender wakes up in bed with a dead female petty officer and claims this was not the woman he came home with, despite the fact that he was drunk at the time. DNA tests reveal that he was telling the truth, but the team must still work to figure out whether this means that he didn't kill the dead woman. The victim's sister and a local corrupt businessman may know more than they are telling. Guest Starring Mýa. |
| 40 | 2x17 | "An Eye for an Eye" | March 22, 2005 (2005-03-22) |
| When a Petty Officer working in Intelligence receives a pair of cobalt blue eyeballs in the mail, the NCIS team starts investigating the case. The sailor commits suicide during the investigation and after Abby matches the eyes to a South American girl in a photo with the dead man's lecturer, Todd and Tony must travel to the Triple Frontier destination of Paraguay to discover the truth. |
| 41 | 2x18 | "Bikini Wax" | March 29, 2005 (2005-03-29) |
| A Virginia Beach bikini contestant drowns in a public bathroom toilet. When the team discover she posed partially naked in a magazine, and was pregnant at the time of her death, clues are revealed that lead to an unlikely suspect. Tony finds a juicy secret from Todd's past. |
| 42 | 2x19 | "Conspiracy Theory" | April 12, 2005 (2005-04-12) |
| The team investigates a suicide case, believing that the main reason of her death is a nervous breakdown, but Ducky believes that she was actually murdered. FBI Special Agent Fornell helps them in the investigation. The team discovers that the dead woman was involved in a love triangle and that this may have contributed to her death. |
| 43 | 2x20 | "Red Cell" | April 26, 2005 (2005-04-26) |
| A marine is found murdered on the school campus, and the team immediately finds a suspect. However, they are forced to start again when they find the suspect murdered. McGee and Abby discover a trace in the e-mails, called "Red Cell," which leads them to believe that the marine must have been involved in a serious death game. |
| 44 | 2x21 | "Hometown Hero" | May 3, 2005 (2005-05-03) |
| The executor of a petty officer's will discovers the skeletal remains of a missing girl in the dead man's rented storage unit. As the petty officer is up for a silver star, it is very important that NCIS determines if he was a murderer, within 24 hours. Soil samples and further forensics lead Abby to discover that if the marine was the killer, he could not have acted alone. Tony and McGee find CCTV footage that suggests the marine was entirely innocent. Tony also has to deal with his car being stolen. |
| 45 | 2x22 | "SWAK" | May 10, 2005 (2005-05-10) |
| When Tony opens a mysterious letter thinking it is for him, a small puff of white powder comes out, releasing a possibly deadly bacteria. Todd calls for help and as a precaution, she and Tony are put into a bio-hazard isolation room. While McGee and Gibbs are determined to discover who sent the envelope and how to cure their friends before its too late for them, Tony's health gets worse. |
| 46 | 2x23 | "Twilight" | May 24, 2005 (2005-05-24) |
| While the team investigate a double murder out on the highway, Todd pushes Tony down and he notices a bomb on the car, saving Todd and McGee. The FBI notifies the team that Ari Haswari has returned to the US and may be on a personal vendetta to assassinate Gibbs. While Gibbs, DiNozzo and Todd search for Haswari, Todd takes a bullet in the chest for Gibbs. She reveals that she is wearing a bullet proof vest but is then shot in the head and killed by Haswari, who is using a Bravo 51 rifle, which is also known as a "Kate". Gibbs and DiNozzo are left shocked and searching for the killer, and Gibbs whispers "Ari" before the end of the episode. |
