Pedro Hernandez was a Mexican drug dealer responsible for murdering Leroy Jethro Gibbs's first wife Shannon Gibbs and their young daughter Kelly Gibbs which occurred while Gibbs was fighting in Desert Storm in or around 1991.
While Gibbs was aboard, Shannon witnessed Hernandez shoot one of his associates, a Marine near Camp Pendleton in San Diego, California. This prompted NIS- (which was NCIS's original name at the time) to place both Shannon and her daughter, Kelly, into protective custody as a means of protecting them until it was time to testify against Hernandez.
Unfortunately, Hernandez struck by shooting the NIS agent driving the car with Shannon and Kelly in it in the head. The unnamed NIS agent died instantly with the resulting crash killing both Shannon and Kelly too. Gibbs was informed of the deaths while serving in the War and was left devastated and grief-stricken. After being wounded, he returned to the US where he met the NIS agent investigating the case: his future mentor, Michael Franks who told him that Hernandez had fled to Mexico, possibly to escape being prosecuted for the killings but while his fate remains unknown, only a few people including Gibbs and Franks themselves know what actually happened.
In a flashback in Hiatus Part 1 (episode), it was revealed that Gibbs after discovering a folder on Hernandez headed to Mexico. In his grief-stricken state and consumed by nothing but a strong, overwhelming desire for revenge against the man who had robbed him of his family, Gibbs killed Hernandez by shooting the other man through the windscreen of his truck with a single sniper shot, the impact of which killed Hernandez instantly and even caused blood to appear on the windscreen. Gibbs later returned to the U.S where he kept the crime concealed for twenty years.
In Hiatus Part 2 (episode), Donald Mallard reveals to NCIS Director Jennifer Shepard that Gibbs would have pursued the killer to Hell and back and told her to close the case because Gibbs got his revenge.
Two investigations into his death were carried out, but neither were ever finished as Lara Macy, while working for the army, investigated his death first, before the show started. Gibbs was her prime suspect, but she eventually buried the evidence deciding that it was a just killing, something that would eventually cost Macy her life as she was murdered by a member of the Reynosa Cartel several years later.
Paloma later the leader of her own cartel as well as a powerful Mexican drug lord while Alejandro became an official for the Mexican Department of Justice.
Through different methods, they attempted to bring Gibbs to justice and ensure that he paid for robbing them of their father but their plans ended in failure and as a result, Paloma is now dead while Alejandro is in jail, having killed Paloma by accident.
Abigail Sciuto was brought to Mexico by Alejandro Rivera who, unbeknownest to everyone at NCIS, even Gibbs himself, was actually Hernandez's son. He told Abby that she was there to teach a class on forensics and that a cold case was chosen at random for her to use as a case study. The case was Pedro Hernandez's murder.
Through hours of research, Abby secretly discovered that Gibbs had killed Hernandez and wrote a forensic report after having the body brought back to DC for Ducky to do the autopsy on. Gibbs being an honest man, told Abby to send her report to Rivera, saying that he wouldn't want her to lie for him.
The report was intercepted by Margaret Allison Hart who didn't want Gibbs to go to jail. After Rivera was tricked into murdering his own sister and ended up in jail, Vance personally filed the report in Annex.
Once again the case went cold, presumably this time for good.
- Unnamed associate- (shot to death).
- The car shooting (three fatalities):
In the episode Life Before His Eyes (episode), it was revealed that Gibbs would actually have been far worse off had he not exacted revenge by murdering Hernandez, as he would have become a drunken recluse who would have pushed away any attempt of his friends trying to help him overcome his guilt.
Coincidentally, Pedro Hernandez is also the name of the prime suspect in the Etan Patz kidnapping case.