It is also is also the last ever episode of the entire NCIS series to feature Lauren Holly (Jennifer Shepard) in the opening credits as well as a series regular.
As NCIS struggles to come to terms with the news that one of their own is dead, Gibbs and the NCIS team attempt to find a motive for the killing while trying to deal with their own emotions over what's happened.
The episode opens with a recap showing the events from the previous episode and then ends with NCIS Special Agent Anthony DiNozzo and his partner, Mossad Liaison Officer Ziva David arriving at the diner and discovering the carnage inside with NCIS Director Jennifer Shepard being among the dead.
A few hours later, Leroy Jethro Gibbs has arrived outside Los Angeles and is heading for the diner located in the Mojave Desert where he orders someone, presumably Tony or Ziva to wait there and that he'll come to them before hanging up his cell phone.
He soon arrives at the diner and upon getting out of the car, sees Tony and Ziva bringing things out from the diner.
Gibbs then rounds on DiNozzo, angrily insisting that he said for them to wait.
As this happens, another male voice stating, "And I said not to" emerges and as this happens, NCIS Assistant Director Leon Vance appears with Vance telling Gibbs that this is his crime scene before removing his gloves.
After they've exchanged greetings, Vance reveals that when Gibbs called SECNAV, the SECNAV then called Vance.
As Gibbs looks as DiNozzo, the other Agent is still guilt-ridden over failing to protect Jenny.
Gibbs then turns and heads into the diner while Vance states, "I'm sorry, Jethro".
Inside the diner, Gibbs takes in the full extent of the crime scene and notes that the bullets used have already been bagged, tagged and processed.
He then spots blood on the floor which was where one of the bodies was and then heads over to where Jenny's body was found.
Vance tells Gibbs that the bodies were flown to D.C last night and that Ducky will be handling the autopsies.
Vance then gives Gibbs a detailed description of what happened, presumably from the evidence found at the crime scene. He tells Gibbs that the four men split into two groups and entered from both sides of the diner.
He then heads over to a spot, declaring that this was where Jenny stood when the gunfight began and that the first shooter never got a chance to fire his gun.
It then cuts to a flashback from Jenny's point of view where the first shooter who enters the diner is shot dead almost immediately.
Vance then points out that Jenny got hit right after that and it cuts to Viggo Drantyev firing a shotgun at Jenny. Despite this, Jenny keeps shooting and Viggo soon goes down.
In the present, Vance recounts that Jenny took one bullet in the shoulder and another in the arm before moving to the side door where the other two gunmen came in.
Intercut with flashbacks, Vance then tells how Jenny took the second and third shooters down before Viggo who managed to survive produces a spare gun and begins firing at her.
Using her last ounce of strength, Jenny soon manages to kill Viggo before succumbing to her injuries and dying seconds later.
As it cuts back to the present, Vance remarks that Jenny put up one Hell of a fight.
"Not good enough", Gibbs grimly replies.
Vance tells him that Jenny was outnumbered five to one.
After Gibbs has told Vance to recheck his math, Vance shows Gibbs four .45 slugs but no .45 gun and tells Gibbs that someone walked out of the diner, alive.
It then cuts to the back of the diner where Vance is stating that there was a second drive which was the Director's rental.
A few meters away, Tony and Ziva are working on the tyre track.
Vance then informs Gibbs that they're going to put out a BOLO as soon as they can ID the car and remarks that he's sure that Gibbs wants to get this bastard as bad as Vance himself wants to.
Vance's cell-phone rings and as he walks away to have a private talk with the person at the other end of the line, Gibbs silently gestures for Ziva to approach him.
She does and when he asks her what they've got, Ziva apologizes.
Tony then tells Gibbs that they haven't got much and that the tyre tracks are from a second vehicle before telling Gibbs that they should have trailed Jenny given Ziva's warning that something was off.
Gibbs remarks that they were an order and that they followed it.
"And Jenny's dead", Ziva grimly remarks.
Vance ends the call and tells the team that it's a cover-up. He then announces that he's heading back to D.C with the bodies while ordering Gibbs to stay and oversee the investigation.
Unsurprisingly, Gibbs passes the investigation off to DiNozzo and then orders DiNozzo to call him before Gibbs heads off, leaving Tony and Ziva behind at the diner to presumably finish processing the scene.
A while later, Gibbs arrives at the gas station Tony and Ziva were at in the previous episode and is busy putting petrol into his rental when another car pulls up.
Gibbs remarks to the person that they're too late.
As he gets out, Michael Franks remarks that that's the least of his problems.
Gibbs gives him the bad news by informing that Vance knows that someone else (Franks) was at the diner.
Franks then announces that he's not the only one problem and then tells Gibbs that Jenny died protecting someone.
"Who?", Gibbs demands impatiently.
"You", Franks replies.
It then cuts to Gibbs who looks shocked at the news.
- Following the conclusion of the case, Leon Vance is promoted to NCIS Director, officially succeeding Jenny Shepard.
- When McGee accepts a phone call from Tony, his phone shows the time of 9:35 A.M and in the next scene, when McGee gets a call from Gibbs, the time on Gibbs's phone shows 11:17 A.M, implying that this takes place in the morning and that two hours have presumably passed since the first phone call.
- The "Previously on NCIS" recap which is seen in the TV version of this episode is missing from the Region 2 DVD version of this episode, simply due to the fact that on the Region 2 DVD, both Judgment Day Part 1 and Judgment Day Part 2 are edited into one single episode under the title, "Judgment Day" with the full episode clocking in at 1 hour and 23 minutes.
|Leroy Jethro Gibbs||Mark Harmon||NCIS Special Agent in charge of the NCIS Major Case Response Team.|
|Anthony DiNozzo||Michael Weatherly||Senior Special Agent and second-in-command of the NCIS Major Case Response Team.|
|Ziva David||Cote de Pablo||Mossad Liaison to NCIS and also a member of the NCIS Major Case Response Team.|
|Timothy McGee||Sean Murray (actor)||NCIS Junior Special Agent and a member of the NCIS Major Case Response Team.|
|Abigail Sciuto||Pauley Perrette||Forensic Specialist, NCIS.|
|Jennifer Shepard||Lauren Holly||Director of NCIS. Died from injuries sustained from a gunfight that took place during the previous episode.|
|Donald Mallard||David McCallum||Chief Medical Examiner, NCIS.|
|James Palmer||Brian Dietzen||Assistant Medical Examiner, NCIS.|
|Debra Green||Sheila Frazer||ZNN Reporter.|
|Michael Franks||Muse Waston||Former NIS, NCIS Supervisory Agent.|
|Leon Vance||Rocky Carroll||Assistant Director, NCIS. As a result of Director Shepard's murder, Vance is later promoted to NCIS Director, resulting in him becoming Jenny's replacement.|
|Viggo Drantyev||Oleg Taktarov||Natasha's Lieutenant.|
|Jasper Shepard||Webster Williams||Jenny Shepard's deceased father. Archive footage. Uncredited role.|
|Svetlana Chernitskaya||Kathleen Gati||Posing as Natasha Lenkov, she was the girlfriend of the Russian arms dealer slain by Gibbs in Paris many years ago. Attempts to kill Gibbs, only to die after being shot in the back by Mike Franks.|
|File Clerk||Mike Muscat||File Clerk at NCIS.|