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Pacci's career came to an abrupt and very tragic end when in March 2004 and during Dead Man Talking (episode), he was shot and killed by a suspect, leaving his NCIS colleagues, Gibbs especially devastated.
Not much is known about Pacci's career with NCIS or what he did before he joined the agency. Shortly before his death Pacci investigated the disappearance of Petty Officer Third Class Carolyn Figgus but his case went cold due to a lack of evidence and possible leads.
Eighteen months after her disappearance and a while or so after Pacci's death, Figgus's remains were found at an abandoned house in an area of the Norfolk Naval Base. Gibbs and his team took over the case and eventually solved it, closing for good during the Season 2 episode, The Good Wives Club (episode).
NCIS Season 1
Pacci's final case before his murder was the investigation surrounding the theft of ten million dollars by Lieutenant Commander Hamilton Voss who had then died in a car crash.
Pacci also attempted to ask Leroy Jethro Gibbs for help during UnSEALeD (episode) but due to the fact that Gibbs and the Major Case Response Team were trying to find a Navy SEAL who had escaped from Leavenworth, Gibbs was forced to turn him down although Gibbs later ending up regretting that decision after learning of Pacci's death.
During the course of his own investigation, Pacci was brutally murdered after being shot in the neck with a single bullet. This in turn eventually caused him to bleed out and he died in a lift with his attacker later disemboweling his remains as they were searching for something but they were forced to flee due to the alarm system going off.
The local cops, upon finding Pacci's body learnt that he was an NCIS Agent which resulted in Gibbs and his team of Anthony DiNozzo and Caitlin Todd being called to the scene. They then took over what Pacci had originally started with the help of Norfolk NCIS Special Agent Timothy McGee.
After intense searching, it was later revealed that Voss had actually faked his own death in the car accident and had undergone a sex change, becoming a woman by the name of Amanda Reed and then gone on to shoot Pacci in cold blood, presumably to ensure that his past deeds which involved stealing money from the Navy went unnoticed.
Reed later met and befriended DiNozzo who like the other members of his team at the time was unaware of Reed's true identity. Luckily, Abigail Sciuto who had been going through Reed's trash eventually discovered the truth: that Amanda Reed and Hamilton Voss were the same person. She later informed Jethro Gibbs and Kate Todd of her findings with both Agents immediately rushing to capture the murderer before any more damage could be inflicted.
Things soon came to a head in a bar where Reed attempted to kill DiNozzo in order to keep her secret safe but Gibbs got there just in time and shot her dead, getting revenge for Pacci's demise.
NCIS Season 8
Pacci appeared in a flashback in the Season 8 episode, "Baltimore" which detailed the story of how Tony DiNozzo went from being a Homicide Detective with the Baltimore Police Department to an NCIS Special Agent.
In 2001, he gave Gibbs the ballistics information needed for a money laundering case that Gibbs working working undercover on that had intersected with the Baltimore Police Department which was how he met DiNozzo.
He also gave Gibbs DiNozzo's personnel file which would later be used to recruit Tony to NCIS. After making his delivery, he told Gibbs that he was going to the infirmary due to his ulcer acting up again and that his stomach would be the death of him, ironically foreshadowing his own death.
NCIS Season 12
As NCIS Special Agent Ned Dorneget's body was being brought onto the tarmac of an airstrip during The Lost Boys (episode), Gibbs looked over and saw Pacci's ghost standing there along with the ghost of people from Gibbs's past including Agents Caitlin Todd and Paula Cassidy as well as Gibbs's mentor, Michael Franks and Gibbs's former girlfriend and partner, NCIS Director Jennifer Shepard.
Leroy Jethro Gibbs
Gibbs considered Pacci a friend, and felt a great deal of guilt over Pacci's death. Pacci had come to ask Gibbs for help with the case in the previous episode ("UnSEALed"). Gibbs hadn't been able to help, as he and his team were busy tracking a Navy SEAL who had been sentenced for murdering his wife and a cable-repairman and who had escaped, seeking revenge on the person responsible for framing him.
Gibbs felt that his failure to listen to Pacci had contributed to Pacci's untimely death. Gibbs was so devastated by Pacci's death that he refused several requests to speak at Pacci's funeral. The NCIS Director eventually took up the task instead. Gibbs soon avenged his friend's death by shooting his killer, Commander Voss/Amanda Reed.
Four years before the events in the Season 2 episode, SWAK (episode), Cassie Yates was serving her time as a "Probie" under the supervision of Pacci. One of the cases they investigated was a rape case involving several midshipmen who were celebrating their graduation from the United States Naval Academy.
It later returned when the victim's mother, distraught over not having justice served for her daughter, sent an envelope laced with plague to NCIS Headquarters which wound up in the hands of Agent Tony DiNozzo and caused the entire building to be shut down while DiNozzo and his colleagues were checked to see if they had any traces of the plague in their system. DiNozzo's blood-test was positive and he was placed in quarantine but eventually recovered from the illness altogether.