The NCIS Hostage Crisis was a crisis that occurred in the NCIS building in March 2004 when the NCIS Chief Medical Examiner, Dr. Donald Mallard, his Assistant Gerald Jackson and later NCIS Special Agent Caitlin Todd were all taken hostage by an unidentified gunman who was later revealed to be Mossad agent Ari Haswari.
NCIS received information from Paula Cassidy, a fellow NCIS Special Agent stationed in Guantanamo Bay or "Gitmo" of a planned terrorist attack against the Norfolk Naval Base.
As such, the main NCIS Major Case Response Team who were stationed in Washington D.C. and led by Special Agent Leroy Jethro Gibbs were given the assignment of capturing Yasir Qassam, a target who had been positively identified by a detainee in Gitmo who had links to Al-Qaeda in the hope that NCIS would interrogate Qassam with Qassam disclosing information about the suspected attack.
In order to capture Qassam, the NCIS team staged a check at the Norfolk Naval Base but one of the security guards ended up having his weapon pulled, presumably by Qassam himself who had noticed that the check was not routine.
This ultimately resulted in Gibbs being forced to shoot Qassam dead.
Qassam's body and personal belongings as well as evidence gathered from his room on the Norfolk Naval Base were all later brought to NCIS so that a investigation could be opened.
However, a Hamas group possibly in D.C. sent an anonymous gunman (Ari Haswari) to NCIS albeit secretly in the hopes of retrieving all the necessary items that NCIS had taken including Qassam's body and personal belongings. They presumably did this out of fear that they would be exposed and as such, wanted to maintain secrecy as much as possible.
Knowing of the risks that awaited him if he were caught such as being arrested or maybe killed in a gunfight between himself and NCIS agents, Ari presumably accepted the mission anyway and later opted to enter NCIS via the morgue which he achieved by hiding in a body-bag.
Upon receiving a call from the Israeli Embassy, Gerald collected the supposed remains and brought them back to the NCIS morgue with Ducky later joining him.
The two opened the body-bag and were immediately taken prisoner by the gunman (Ari) who held the two men hostage for a few hours while even ordering to examine the body as well with all three wearing the necessary breathing gear as Qassam's body was presumably considered dangerous.
Under gunpoint, Ducky requested that Forensic Scientist Abigail Sciuto bring down all the evidence to the morgue which Abby agreed to.
Unfortunately, due to her constant phobia of the morgue which included visions of seeing herself lying there in the morgue, sometimes dissected, Abby relented and headed upstairs to meet Kate whom she begged to take the evidence down to the morgue due to Abby's own autopsy phobia.
Kate did so but wound up getting caught and becoming the third and final hostage of the crisis.
As punishment for being lied to, the gunman responded by shooting Gerald in the left shoulder, greatly leaving Gerald injured while leaving Ducky and Kate horrified.
The two later treated Gerald despite the fact that the morgue lacked the necessary equipment to treat Gerald's wound.
Having figured out that something was wrong, Gibbs and his second-in-command, Senior Special Agent Anthony DiNozzo took action while the rest of the building was evacuated albeit secretly and presumably not to further aggravate the situation with only four agents, Gibbs, DiNozzo, Christopher Pacci and Balboa being left behind to co-ordinate the rescue operation while the FBI's Hostage Retrieval Team was called with the team eventually arriving on site.
Gibbs later engaged in a stand-off with the mysterious terrorist/Ari that turned into a duel which ended with Ari shooting Gibbs in the left shoulder.
Seconds later, the FBI HRT team entered the morgue while Gibbs later lost consciousness altogether.
Gibbs eventually regained consciousness to find the morgue in chaos and soon discovered that he'd actually shot the dead terrorist instead of Ari.
Gibbs survived being shot in his right arm but was forced to wear a sling for the time being and although the wound itself eventually healed, Gibbs was left with a psychological pain in his right shoulder and over the next few months, soon developed a very strong determination and later, obsession towards finding out who the mysterious gunman was.
Having failed to retrieve the belongings and ultimately failed his mission, Ari was forced to flee NCIS Headquarters and the Navy Yard in order to avoid being captured or worse, killed. He did so by fatally shooting an unnamed H.R.T. agent before stealing the dead agent's uniform which he soon used as a disguise.
This in turn got him past the security guards and enabled him to escape with a Mossad extraction team meeting him along the way. Among the members of the extraction team were Ari's half-sister and control officer, Ziva David as well as future former Mossad operative Namir Eschel.
Gerald, Kate and Ducky were all eventually rescued from the morgue with both making a full recovery although the events left both Gerald and Kate deeply traumatized.
Unable to cope with the psychological efforts that resulted from being taken hostage and no longer feeling secure in his job, Gerald later temporarily stepped down from his position as NCIS Medical Examiner Assistant before heading to rehab for the rest of the year. He was replaced at first by Jason Patel and later by James Palmer.
A year later and a week before he was due to return work, Ari kidnapped Gerald which in turn had Gerald resigning from NCIS for good with Palmer later permanently taking over the role of NCIS Medical Examiner Assistant as a result.
Kate was left deeply guilt-ridden over her failure to stab the terrorist with a scalpel. Unfortunately, this unwillingness and hesitation to do so would later prove to be her own undoing and ultimately cost her her own life when she was shot dead by Ari just over a year and a half later during the NCIS team's attempt to stop Ari and his second and final terrorist cell from launching an attack on Navy ships coming into dock at Norfolk Harbor.