Po smrti Shepardové se novým ředitelem NCIS stává Leon Vance. Ziva spolupracuje s Mossadem, Tony slouží na letecké námořní lodi, McGee je převeden na jiné oddělení a Gibbs velí novému, poněkud nesourodému týmu složenému z agentů Keatinga, Langera a Leeové. Všem se stýská po starých časech a rádi by opět pracovali spolu.

Nový tým se zabývá nálezem mrtvoly muže, identifikovaného jako Steven Nicholas Vargo, jenž pracoval ve strategickém plánování a měl jednu z nejvyšších bezpečnostních prověrek. Je pohřešován již čtyři měsíce a usmrtil ho jediný výstřel ve spánku tlumený polštářem. Keating nalézá spojitost mezi tímto mužem a Brianem Robertsem, jenž byl zabit při nedávné explozi bomby v jednom z barů v Maroku...

Mark Harmon says: "Previously on NCIS" and we see Final scene of season 5 final ep: reminds us that McGee was reassigned to Cyber Crimes, Ziva sent back to Mossad and Tony to USS Ronald Reagan as Agent Afloat. Vance hands over three files to Gibbs and tells him to meet his new team.

Cut to backless dress view of Ziva in nightclub singer mode, singing about “Temptation”, which has a chorus of “Don’t assume” which she is singing as various members of the audience are rising and leaving their tables. She is clearly getting distracted by this: her eyes flick to an attaché case under a table, almost hidden by the tablecloth.
As her eyes narrow in suspicion, the case goes bang. Ziva is blown off her feet.

Roll opening credits.

Scene: 4 months after the Season 5 last show, in the bull pen with the "Gibbons". The new agents, the Gibbons who have replaced our beloved Giblets, are in the bull pen, at the desks of the Giblets. We see Langer (of FBI whom we have met previously and worked with Gibbs, Lee (lawyer agent who has been a pain to Gibbs in the past, although she did rescue Chinese illegal immigrants by going undercover, almost successfully) and Keating (curly haired geek wannabee McGee) are in the office without Gibbs.

Phone is ringing. Keating (at McGee's desk) is typing hard and fast. He is annoyed by the unanswered phone on DiNozzo's desk. He pauses, sighs and asks Langer “You wanna get that?” Langer has his feet up on the desk. Langer sighs, and picks up the phone: it is for DiNozzo again. He starts to explain to the caller that DiNozzo has been reassigned and to try calling the personnel officer. The caller hangs up.

Langer: “Four months I’ve been sitting here fielding calls for DiNozzo and I swear they are all women!” Lee (at Ziva's desk, searching hard for something she cannot find): “And that surprises you? Have you seen my Oman threat assessment?” Langer, in fake surprise: “Oh, is that what this is? And here I thought it was a travel brochure….” (Argy bargy over the file ensues between the three.) Keating says “Give her the file Langer”, as Langer holds it out of an annoyed Lee’s reach. Gibbs enters without being noticed and repeats, in a tired tone, “Give her the file Langer”. They are all caught. As chorus of “good morning sir” breaks out, Lee and Keating stand in his presence. Langer, slowly, belatedly, begrudgingly follows suit. Gibbs makes a snarky remark about having established what kind of day it is, asks for the threat assessment and Lee rushes to hand it over, knocks the file off Langer/DiNozzo's desk, onto the floor and spills all the pages, falls to her knees to pick them up, as does Keating. Langer sends a disdainful look at Lee and complicit look to Gibbs, who frowns until Langer starts helping his colleague. Lee is apologising to 'Sir' until Gibbs says “What did I tell you about calling me Sir?” “Sorry….Gibbs”.

Keating, anxiously probie in style, points out that there was an urgent phone message, even as Gibbs is reading the bright yellow message and starting to pick up the phone to return the call. Gibbs makes a snarky (sarcastic) remark to Keating whilst dialing. Gibbs talks on phone. Gibbs hangs up and tells them to grab their gear. (The tone/mood shows that they are uncomfortable with Gibbs and he is exercising great patience with them.) The team takes an unconscionably long time to “grab their gear” and rush to the lift, letting the doors shut just as Gibbs goes to step into the lift. He stops, looking at the closed doors: the doors reopen with a chorus of apologies and Langer blaming Lee, who confesses she “was pressing the wrong…thing”. He gets in, silent, turns around rolls his eyes and just puts up with it.

At the crime scene: Trailer park. Red haired middle-aged park manager points out that it’s the type of place where everyone makes sure they don’t notice anything. The body has been there four months (paid in advance) so the body was never found. The team have been going through the marine’s personal effects, photographing and tagging and bagging. They banter/bicker amongst themselves. Langer is called to report Gibbs on what they found out about the victim. Petty Officer Stephen Nicholas Vargo, worked on the Navy yard in strategic planning, in the building next to NCIS HQ. Went missing 4.5 months ago. Security clearance was as high as they go. As Gibbs walks in, Ducky is saying “Mr Palmer, tell Gibbs that he can send in the B team”. “Implies there’s an A-team, Duck”. “Isn't there?” “They’re all A teams” “Perhaps some even A-plus.” The body is in bed. Palmer makes a bad joke about the person coming to a “sticky end” because he was naked in bed and dead. Single gunshot wound to the upper temporal area. Probably while he was asleep. Pillow must have been held to his head to muffle the shot. Bled out. The stench must have been incredible. Isn't anybody curious anymore? Gibbs says “Bled out. Like him” (looking at the body).

Gibbs in Abby’s lab: metal music playing
"Gibbs!"
"Abby?"
"I need a hearing test…" she explains that her hearing must be going because she didn’t hear the elevator. He says “Stairs”. She is shocked and accuses him of avoiding the elevator because he associates the elevator with people he is trying to forget. “I’m not trying to forget anyone”. (This is said meaningfully. She gets it. She turns to business).

Abby’s lab: the forensic discourse (clues to you and me) "9mm casing. The slugs are hollow points, of a type that is used by a bunch of federal agencies including NCIS and its not the type of slug that Joe public can get his mitts on." (highly paraphrased)
Abby’s lab: The 126 days conversation
G: “What else?”
A: A number (she tears a post-it note off a poster of a sad face)
G: 1-2-6
A: One hundred and twenty six: that is the number of days that Tony, Ziva and McGee have been gone. I really didn’t think you would let it get into triple digits Gibbs but now its way more. Its like a third of a whole year. I miss them.
G: Abby, you had lunch with Tim yesterday.
A: Its not the same. I miss them collectively, as a group, my three musketeers. Tim is the only one I’ve seen. No Tony, no Ziva. I get postcards from Tony. I want them back Gibbs (HUGS GIBBS) Please get them back. (He looks pained but pats her back, silent. She springs out of clingy hug and fixes him with narrowed, steely hard stare: he semi-smiles).
A: You have 10 days. (Gibbs looks slightly surprised by this aggressive command so she relaxes her face a little and relents) Ok, I don’t want to pressure you: so 12. (She narrows her eyes again...) But no more than two weeks. (Gibbs enters into a minor staring contest with her and, seeing that she is not giving ground, looks away, then turns and walks off, seemingly thinking discretion is the better part of valour with Abby in this mode and seemingly semi-compliant. She has a parting shot...) “And stop taking the stairs!” (She remains standing, listening, cocks her head to one side, eyebrows raised, wondering whether he will obey, hears the “ping!” of the elevator. She looks satisfied and smiles to herself) .

In the bull pen: Keating at computer has news for Gibbs. He found a connection between a Petty Officer Roberts and PO Vargo, the body that they found. Roberts was blown up in Morocco overnight. Gibbs stands in front of the plasma screen and tells him to "put it up"...and then has to clarify "on the plasma, Keating". Roberts got out of the Navy 6 months ago. Lee asks "Terrorist attack?" and Keating says he is "trying to get more now...got a link to the raw feed from ZNN" Langer says "Unlikely coincidence" as they start watching the TV feed: then Langer says "oh my god, isn't that.." and Lee breathes "Ziva". Keating freezes the picture on a closeup of Ziva on an ambulance stretcher. Gibbs instructs Keating to get Ziva on the phone. Keating looks scared and says "I'll try" but Gibbs has already departed and clearly won't accept "tries" instead of "does".

In the cyber crimes unit, we see McGee with his co-workers calling him boss as they plague him with questions. He gives them short, sharp instructions, as he keeps typing away on his own work. Suddenly he hears a quiet voice say "Boss?". McGee stops typing, turns, stands and looks in wonder and says "Boss?!?" McGee's co-workers are gawking until McGee looks sideways at them and they hurriedly return to their terminals. McGee explains that he is not really their boss but they call him that because he is a field agent and carries the handgun. Gibbs asks has he heard from Ziva and McGee says he gets an email every week until three weeks ago. Assumed she went on vacation. Gibbs says "try undercover" and McGee says "that would fit".

The phone call with Ziva: Keating phones down to Gibbs and starts explaining how he managed to track down Ziva by phone by contacting someone he knows at Pine Gap which is the secret communications base that USA has in outback Australia...but Gibbs just says "put her on". Gibbs talks to Ziva: we see that she is in an office at Mossad HQ and talking on hands free so that an older man and a young bearded man can hear too. Gibbs asks how she is, and notes that he saw her on ZNN. She explains what she was doing undercover: trying to get the attention of someone who had an unhealthy interest in a Chechnyen terrorist group. Gibbs asks is it Roberts? She asks what he knows. She says they think Roberts was the target of the blast, not other known terrorists in the room. Gibbs asks "Who tipped you off?" Ziva looks uncomfortable and says "Director Vance". (PROFOUND SILENCE FROM GIBBS. EVERYONE UNCOMFORTABLE).
Gibbs just says, quietly but truly, "We miss you, Ziva". She steps forward, puts the phone on private and picks up the handset "I miss you too. All of you. Even...(clears throat) Tony. Take care, Gibbs."
"Yeah. You take care too." They hang up.
The older man with Ziva speaks: "Ziva, go home. Rest." She starts to leave, and the younger, bearded man stands as if to follow (her bodyguard?). He says "A kiss for your father." She returns across the room as the younger man looks discomfited, bends down, kisses his cheek and murmurs "Goodnight Papa" and makes to move away. He catches her face between his hands and looks hard. She remains unsmiling, straightens up, leaves.

Gibbs confronts McGee: Steve Vargo. What do you know about him?
McGee: Boss, I'm not exactly sure I can tell you what I know... Orders.
Gibbs looks at him, purses his lips, points a finger upwards and raises his eyebrows. McGee says "Yeah".
Gibbs nods, pats McGee's cheek in farewell and leaves. McGee just stands, clearly torn between orders and the urge to please his Boss. McGee's underlings are watching avidly. McGee stands, dejected. They ask "You OK, boss?" and McGee pulls himself together and murmurs "Get back to work". They spring back to their keyboards with a "Yes boss!" "Hey boss".

Gibbs confronts Director Vance and learns about Muhammad Ali v Sonny Liston, knockout in 1965
Closeup shot of Muhammed Ali standing over Sonny Liston, in the 1965 fight. Vance is explaining how Ali knocked out Liston in the first minute. "Ali hit him, Sonny went down, then stayed down. All hell broke loose". Lot of people thought it was fixed, thought Sonny Liston took a dive. (The camera has been pulling back, until we see that we are in the Director's office, and Vance is talking to Gibbs.) Gibbs asks whether Vance thinks Liston threw the fight and Vance says he thinks it is easy to jump to conclusions without having all the facts. Vance looks Gibbs in the eye and says "swing away".

Gibbs says "You didn't break up my team over Jenny's death."
Vance: "No. Five months ago I got a series of anonymous calls from a Navy PO (Vargo). He wouldn't say what sort of data he was being blackmailed to steal. I [Vance] went to DC to meet him but he never showed. Whoever was blackmailing Vargo was an NCIS agent.
Gibbs: "Not one of mine."
Vance: "No, I narrowed it down to three agents. Only reason I broke up your team was to form a new one so that you can help me find out which one of these three...." (He clicks on CCTV of the bull pen, where Langer, Lee and Keating are working) "...is betraying his country".

Gibbs: "You were going to get around to tellin' me?"
Vance: "I've got no evidence. I figured I put you with them your radar would go off so that one day you'd come to me and say you had a doubt about one of them."
Gibbs: "A doubt? A doubt Leon? I got a doubt about every one of them! I got a former FBI guy who doesn't listen, a boy genius who doesn't drive and a lawyer who doesn't shoot!"
Vance: "Langer made the jump to NCIS 8 months ago from FBI ....He used you to get inside the agency"
Gibbs: "Doesn't make him guilty"
Vance: "Just clever."

Vance explains that McGee was put downstairs to work his way through seven layers of encryption, but that after 4 months they've gotten nothing. Mossad mounted an operation to pick up Roberts in Morocco as he was willing to sell the name of the NCIS traitor but they weren't quick enough. And they think that Vargo is dead because it was tying up loose ends.

In the bull pen, the Gibbons are without Gibbs: Langer puts down phone. Vargo's computers have been seized. Keating says "Standard Operating Procedure, it's in the Agent's Manual" and quotes chapter and verse on the law pertaining to seizure of evidence. Langer says "You're making that up". They discuss where the computer will be then and that, if seized, it would have been logged. Keating checks. "It wasn't logged" Lee says legally that creates a problem with the chain of evidence. They consider that it might be "in the evidence locker" and Keating says it will be downstairs with the geeks. The other two just look at him and he says "What?", puzzled (and clearly not seeing himself as one of the geeks).

Enter Gibbs, full of wonder at which one is the traitor, demanding a status report which no one gives, so he gets insistent and then they all speak at once. He is given various bits of information. The bit about the missing computer gets the comment from Gibbs that the computer is probably down in the basement "with the rest of the...." (he looks at Keating, who is wide-eyed, and he refrains from saying "geeks"). Keating looks discombobulated. Gibbs says that he will handle the computer bit and tells the Gibbons "Witness statements!" They attack their computers. He looks sideways at each of them.
Then he looks to the side, into the camera, straight at Vance in the Director's Office.

McGee's Basement, with the McGeeklets saying goodnight boss and waving goodbye.
McGee's team have clearly been bundled off home en mass, and are in the lift, waiting for the door to close, geekishly and excitedly and brown-nosingly waving goodbye and saying "Goodnight boss" and "See you tomorrow boss" in bright tones. Their light mood shows they have no idea why they were trying to break encryption keys for McGee and, through him, Director Vance. McGee stands quietly patient as the lift doors close on the crowd. Gibbs is standing almost toe to toe (and we can see just how tall Sean Murray must be, as Gibbs is looking up into McGee's eyes). Gibbs says "You call him?"
McG: "The Director's on his way down"
Gibbs: "You like working down here, McGee?" (with an incredulous note in his voice).
McG: "Boss, I'm sorry. He made it very clear I was not to discuss this with anybody."
Gibbs: "Wouldn't have stopped you in the past."
McG: "It was different then. We were a team. I would give this up in a heartbeat to be working with you and Ziva again".
Gibbs: "And DiNozzo?"
McG: (looks down, semi-shrugs) "Yeah, him too."
The Director enters from the lift. "You can tell him, McGee,"
They all move to the computer. McGee starts to explain what he was doing and realizes that Gibbs isn't interested in the technicalities. So he tries to explain more simply. And it's still too technical. McGee muses to himself "I really have been down here too long, haven't I". Then he just picks up a memory stick and says a few days ago Roberts downloaded a 2.7gigabyte file onto something similar, but they don't know what file. Vance gives McGee permission to keep Gibbs posted and dismisses him. McGee gets into the lift, after saying "Goodnight Director, Goodnight boss". The lift doors close. McGee's calling Gibbs "boss" and a speaking look from Gibbs is enough to get Vance to say to Gibbs "Solve this, and then we'll talk."
Gibbs says "Ziva too" in a warning voice. Vance departs.

NEXT DAY in Autopsy (which is a much brighter, cheerier place than McGee's encryption cyber geek room)
Ducky enters, and sees Gibbs staring at X-rays on a light box. Ducky says "Good morning Dr. Gibbs."
Gibbs asks "Duck, what's this shadow here?" Ducky says it is a broken jaw (he uses the real medical terms and Gibbs translates it into broken jaw). Caused by a blunt instrument. No sign of a fight. Victim dazed if not unconscious, allowing the assailant to pick up a pillow to silence the fatal gunshot. No surprises, no telltale marks or bruises. Just a rather unrevealing death, says Ducky. "Did I miss something?"
Gibbs says "The pillow!"
Ducky "The pillow?"
Gibbs "The pillow!!" and stalks off to Abby's lab.

Enter Gibbs, bearing Caf-Pow, to Abby's lab where she rather mournfully adds yet another postcard of the USS Ronald Reagan and USS Seahawk (CVN 65) to her collection of Tony postcards. ("Abs!! I really miss you! Love, Tony")
Gibbs: "Abs! The pillow!"
Abs: "The one with the gunpowder, or the one with the blood and the gunshot?"
Gibbs" The one with the gunpowder."
They discuss that there is not enough gunpowder on the pillow to make it an effective muffle for the sound. Gibbs realizes that it was not to silence the sound but to cover the face. The killer was squeamish. Abby discourses on how she can relate to that as she would want to cover the face if she shot someone not that she would but if she did she would want to...(by now Gibbs has departed for McGee's basement lab, having been summoned by phone).

McGee's lab: Apart from Gibbs making a crack about whether McGee wants to wait for the Director, he receives a report that Agent Lee received phone calls from the dead sailor.

Director Vance and Gibbs interview Lee: She says that the caller did not identify himself, she filed a report and forgot about it, as he did not tell her anything worthwhile that could be used. He wanted legal advice because he'd been stealing from the Pentagon and she assumed it was a money scam. No one ever followed it up with her.

McGee is called to Vance's office. They discuss what info to find out about the three agents and cross-checking Lee's story. They ask about encryption progress. McGee says its almost impossible. But he has an alternative way. But it is clear from the silences that it is dodgy. (They do not use the word hacking). They need someone with access to certain files to find out what the bad guys were downloading. "Course, we would have to go through some channels". Gibbs asks "That the fastest way?" McGee says "I was afraid you might ask me that." Vance says "We didn't have this conversation".

In communications suite, McGee does a video con call with TONY!!!!! (Oh Tony, we do miss you!)
"McGoo. It's true. TV really does add 10 pounds. You been hitting the jelly doughnuts again? How do I look?"
"Well, I never thought I would say it and truly mean it, but it's good to see you again, Tony."
"I miss you too, Probie."
"First the USS Ronald Reagan and now the Seahawk. How's life afloat?"
(Tony puts on a piratical Oirish voice): "Ah, life in the ocean blue, me hearties. If the scurvy don't get you, the pox will. And tell me this, me little McShipmate, how is that scurrilous blackhearted pirate king of ours, Captain One-shot Gibbs?"
Gibbs: "I'm just fine, DiNozzo"
Tony, disconcerted: "Oh, ah .....(headslaps himself)...There you go boss, Welcome aboard" (Gibbs nods in acknowledgment)
Gibbs: "Got work to do"
Tony: "I'm on it boss. What am I on, McGee?"
McG: "Are you alone?"
T (incredulous, with a background shot of a busy ship-to-shore com room with lots of sailors phoning home): "Oh yeah. Just me and 5000 of my closest friends. I AM NEVER ALONE." (He leans forward and whispers) "I really need to come home, boss."
G: "Workin' on it."
McG: "The only way we are going to access this information is from a secure Naval communications room, so you are it. I'm going to give you a code and you're going to enter it into the keyboard. When you do, it's going to ask you for a password and an authorization key."

Tony reels back, putting on a happy fake impression to make it sound like he is talking to family, if anyone around him is listening to him, and he makes out as if he is talking to his dad:
Laughs and says LOUDLY, "Dad!, ohhh, This is why I don't want Tim drivin' my car. I told Tim that that's my car and...it's is not a family car, it's my car." Tony leans forward and whispers to the camera "I don't like the cut of your jib, McGee. This sounds suspiciously like illegal activity and ...well...a man of my delicate disposition is not suited to that kind of thing."
McGee: "Don't be such a girl, alright?"
Tony lifts his chin, taking the hit.
McGee: "Ready?" (Tim reads out the code, and Tony types it in).
Tony "Alright, open to search page." (He looks around, and leans into the camera and whispers) "Is this hacking McGee? Are we hacking?"
McGee emphatically: "It's not hacking."
Tony: "But it is illegal, right? Don't answer that. I know its illegal. I'm having fun."
McGee: "Then search parameters...enter the hash symbol..." (more code) (we see Gibbs watching his boys, intent but slightly smiling as they work computer magic)
Tony, noticing someone walking behind him, says loudly "DAD! It's my point exactly dad. It's just not fair." whispers again "Alright, it's searching. Waiting. More waiting."
McGee: "What do you see?"
Tony: "A short life. Yours, if I get caught."
*beeps*
Tony: "Great. Next stop, Gitmo. I got a hit."
McGee: "Download the summary file and email it to me." (Tony types, biting his lip in resignation).
Tony: "Well, it's been great talking with you, Pa. Thanks, Tim. You know I love you guys. It's just that Tim always messes my stuff up. He doesn't know how to shift gears, he doesn't change the oil. Make sure you feed the chickens. Say hello to Mom."
McGee (moving his microphone so that Tony cannot hear, mutters to Gibbs "He's insane". Gibbs, standing very upright, bouncing slightly on his feet, says "Oh yeah!" but almost smiling)
McGee to Tony: "Thank you, Tony. Look after yourself. Don't fall overboard, okay?"
Tony, looks left and right, then mutters: "More likely to jump."
Gibbs: "DiNozzo!"
Tony, puzzled: "Pa?"
Gibbs: "Take care of yourself."
Tony (looks around) "Miss you too, Dad" and signs off.

McGee opens his email. "Oh boy!"
They have found that the file is the DOMINO battle plan for attack in the Middle East, the US response if Israel is attacked.

Vance's office: Vance says that "This is bad." McGee arrives and tells Vance and Gibbs that he has found that Lee visited the strategic planning office each week at the same time. Lee is brought in and says she wasn't meeting Vargo each week. They ask who?

In Autopsy, interrogating Palmer:
Gibbs: Have you been seeing Agent Lee?
Palmer: No! (pauses) Yes! (confused) Not anymore. I was seeing her.
Gibbs: Where?
Palmer: Here. There. Mostly here until Dr Mallard almost caught us. Then we had to change where we did it. (he explains that they used to use the building next door, using the paint locker in the basement). He explains that they stopped it a few months ago.
Gibbs: She stopped it
Palmer (indignant): I stopped it. I felt I was being used. [We can see Jethro make a mental note of this detail.]

Vance's office: phone call brings info that confirms the details and Lee's story, so they eliminate her as the traitor.
Bull pen: Keating realises that someone in Cyber Unit is checking for irregularities in the Gibbons' bank accounts.
Gibbs enters the room and Langer demands to know if he is under investigation. Gibbs points to Keating and orders him to the interrogation room now. He tells the others to not leave the base.
Interrogation room: Keating gets interviewed and mutters "I have rights." Vance asks Agent Gibbs, does he have rights? Gibbs points out that using the right to silence could look bad. Vance interrogates Keating about his computer skills.
Bull pen: Langer looks in Keating's bag, because he is a computer geek whom Langer thinks can do crimes. Lee bends down and pulls out a military pass from Keating's bag, but Keating is a civilian and shouldn't have it. Langer and Lee decide to go and check out the place that Keating had access to.
In the security planning building: Lee is acting nervous the entire time and says that if they get caught, the bosses will think it's one of us. Langer has a sudden realization, looks at Lee, and starts to move for his gun which isn't there. Lee says "What?"
Interrogation: Vance gets a call from McGee that a spybot has detected intrusion into the archives room in the security planning building next door. Call on Gibbs' phone is from Lee: they hear shots and Lee sounds terrified. They run, saying "It's Langer!"
Security planning archive room (which is in darkness) They find Agent Lee, holding the gun, shaking. Langer is dead. Gibbs leans down and takes the gun. He tells her "It's ok". Lee says "It was him. All the time. It was him". Vance pulls out the military access card and says "He's got Vargo's access card". Lee just snivels.

Vance's office: he is on the phone with Ziva's dad at Mossad: They discuss the difficulty of having children that don't see them often enough. ZIva's dad says that he knows people wonder how he could raise his daughter to be a killer, but Vance says he always knew the answer. Ziva's dad says that it is so the generation after won't have to do it. He asks Vance, "Are we winning?"
V: "I don't know, Eli."
Eli: "I like to think we are, but then there is something else...a bomb, an atrocity..." (pause) "You would like her back."
V: "Yes."
Eli: "Use her well, Leon. She is the sharp end of the spear". They say Shalom. Vance clicks on the video of Ali knocking out Liston.

The bull pen. Lee is packing up her stuff.
Gibbs arrives. "Done?"
Lee says "Done. Look. I know you never thought much of me as a field agent. You probably never thought much of me as a lawyer"
Gibbs: "That's more the profession than the person"
Lee: "But if you ever need...I mean, if the chance ever comes up again..." (she is interrupted by her cell phone. She cuts it off)
Gibbs: "It might be important."
Lee: "It can wait. They shake hands. He hands her her stuff and she starts to walk away, but turns and asks "Do we know why he did it?"
Gibbs: "Money ...probably."
Lee: "Well, thanks. Be seeing ya." Gibbs salutes her with a finger to the brow.
Abby arrives with Tim and she is so excited, she hugs Gibbs. Lee walks to the elevator. The doors open, Ziva walks out and Lee says "Hi". Ziva looks around at Lee and is surprised and says, politely, "Hi." Abby yells in happiness at the sight of Ziva. Lee smiles wryly and says "Welcome back." Ziva says "Its good to be back" and goes over to Gibbs, Tim and Abby. As Lee gets in the lift, already ignored by the rest of the team, she watches Ziva give and receive a big hug from Gibbs: Ziva and Gibbs are just locked in the kind of hug you give when you get someone back safe, who was too close to death for comfort, or a long-lost relative. Lee seems to be noticing the disparity in warmth between the farewell she received and the welcome Ziva received. As the elevator doors close Gibbs gives Lee a long look.

Lee in the lift (and THIS IS IMPORTANT)
Lee puts down her box. Picks up her phone. Reads the text message. It says "Do they suspect?"
We get her flashback of what happened with Langer. We see her shoot through the pillow (which is over Vargo's face...she is the one who is squeamish about shooting people). We see her at the crime scene, when she snatches the military pass and puts it in Keating's pocket instead of putting it into evidence. We see her view of the moment when she cold-bloodedly shoots Langer before he has a chance to shoot her, then she goes to his body, picks up the gun and shoots through a glass door (to make it look like he shot at her).

Lee, in the elevator, simply answers the text, "Do they suspect?" with the word: "No"