Gibbs (to Pacci's killer): "His name was Special Agent Chris Pacci. And he was a friend." (Boom, Headshot!)
Gibbs' reaction to finding out the Man Behind the Man was the father in "See No Evil" may just possibly be the most massive FridgeTearjerker in history. After seeing another man ready to throw away what he himself would do anything to get back, nobody can fault him for having a crack in his armor.
In the episode "Heart Break," Kate unwittingly is the 'cop' part of a suspect's Suicide by Cop. Due likely in part to her religious background (coming from a Catholic background), she is clearly devastated not only in the fact that she killed an innocent man but that there's no punishment coming to her, since she was doing her job and attempting to protect Gibbs from someone she thought was a threat.
"Call of Silence" with the Medal of Honor recipient believing he had killed a fellow marine, his best friend, during WWII. Offering his Metropass to DiNozzo (multiple times) and dancing with Kate in the squad room...
DiNozzo nudging aside the man's tie, so that the Marines coming to arrest him could see the Medal of Honor, and them immediately snapping to attention out of respect.
Just about everything with Corporal Yost is a Tear Jerker. He walks into NCIS headquarters, saying he killed his friend, and is practically begging to be arrested for it. And that's just the first five minutes of the episode. His dance with Kate in the squad room makes you smile through the tears, and then there's the flashback that Gibbs triggers to prove his innocence — he struck his friend in the head with the butt-end of his gun because he couldn't stop moaning in pain from having his legs blown off, threatening to give away their position to the Japanese at Iwo Jima. Even Lieutenant Coleman, who's been demanding Gibbs turn him over all episode, is brought to tears and drops the issue after watching him break down in the interrogation room.
Season 2, episode 22, "SWAK". Seeing DiNozzo looking so awful as he's dying from bubonic plague. Granted he DOES live, but still...
Season 2 episode 'Witness', when McGee gets sent on a solo assignment as a test by Gibbs; the task being to determine whether or not a witness's account of a possible murder is credible. Upon meeting her, he discovers she is a graduate of MIT, same as him, and makes the call to bring the rest of the team in to check out the suspected crime scene. As the episode goes on he forms a bond with the eponymous witness, even flirting with her as he stakes out the crime scene/ apartment across the street from hers. Needless to say, when the killer goes to kill her he is quickly on the scene; however in his haste he forgets to clear the room and gets hit in the head for his troubles. His inability to save her or catch her killer at the scene really does a number on him, to the point where when he inevitably realizes who the killer is, his first reaction is to chase him into traffic, then shove the business end of his Sig in the guys face, with a truly frightening expression of rage on his own. The Tear Jerker moment? At the end of the episode he is quietly writing something on his notepad, which Kate and Tony believe is his official report. Instead it is a sympathy letter to the girl's parents, saying how sorry he is for not saving her. Damn.
In "Frame Up": At one point it all the evidence points to Tony as being the killer. At one point Abby is talking about how she must have screwed up and Tony will go to prison because of it, and is clearly on the verge of tears while recounting this to Gibbs. Gibbs responds by kissing her on the hair.
Particularly when Gibbs wakes up with amnesia, and everyone's calling him "Agent Gibbs"...
Gibbs: I'm NOT Agent Gibbs, I don't KNOW Agent Gibbs, I don't WANNA know Agent Gibbs! I want... I want SHANNON! I want... Kelly... (sob) I miss 'em... God, I miss 'em...
Ziva snapping Gibbs out of it.
Ziva: Ari killed Kate. And I... (bursts into tears) I killed Ari. Gibbs: Your brother. You killed your brother. Ziva: Y-Yes. Gibbs:You killed your brother... (tearing up) to save me.
Gibbs' flashbacks of his blissful life with Shannon and Kelly. Then the shot of him sitting on a beach—the same beach where they shared happy times—with a gun at his head. And lastly, the gut-wrenching scream he lets out after killing the man responsible for their deaths.
Speaking of which, Ziva shooting Ari. Gibbs' expression of shock and horror as he realises he put her in a position where she had to shoot her own brother, that light touch to her hand as he walks by, and her mourning song...
Especially when straight after the scene shifts to Kate's funeral.
The end of "Honor Code", where scenes of Gibbs working on his boat with Zach are montaged with scenes of Gibbs and Kelly working on the boat.
When Kate Todd was killed. And her blood splattered on Tony.
And Gibbs' hallucinations of Kate in the next episode. "Why me Gibbs? Wasn't taking one bullet enough for you? Why did I have to take two?!" and "Why did I die instead of you?!"
Notable when compared to the others - everyone else is seeing her offering statements of how it's okay and they're going to be all right, even joking around. Gibbs sees her berating him, yelling at him, angry both in general and specifically at him. It makes the finale, of her in her coffin, gently ribbing him about being late to her funeral, turn the tears to ones of joy.
When Abby is upset in "Skeletons" because her boyfriend dumped her for being too tall. That in itself is sad enough, but the Reality Subtext is sadder still (his dumping her was a hasty rewrite after the actor playing him died).
On an earlier-season note, "Once A Hero" brought the tears, but for a different reason. Firstly, once it was clear what had actually happened and that the deceased Marine had been trying to save a teenaged prostitute before he was killed, and secondly, somewhat cathartic tears once they found all the other girls locked in that van.
Gibbs: His name was Brian Wright. Sergeant Brian Wright. United States Marine Corps. Bronze Star, Purple Heart. He was a hero.
The season four episode "Dead Man Walking", in which Ziva comes to care for a man who's dying of radiation poisoning, definitely yanks on the heartstrings, particularly with the last scene:
Roy: Would you think you'd have noticed... that I was no longer there? That I'd stopped running. Ziva: Yes. I would've noticed... I would have missed seeing you. Roy: But eventually you'd have forgotten me. Ziva: I won't forget you now.
And in later episodes she can be seen wearing his orange watchcap when she's out running.
"Grace Period," from the beginning - Two agents are lured to an abandoned store as a trap and killed, to the shocking twist at the conference - One of the clerics is a terrorist with a bomb strapped to his chest, and Special Agent Cassidy sacrifices herself to stop him. The other shock is just the added Tear Jerker fuel: Gibbs' team was supposed to be the ones to do the case at the abandoned store, and subsequently would have died. The song at the end R.E.M.'s "Everybody Hurts" is just perfect.
Tony finally reciprocating Jeanne's declaration of love. Wrenching enough, even moreso knowing how it turns out.
Any time where Abby is less than sunny is jarring, so seeing her almost in tears going over the late Director Shepard's possessions in the season 5 finale "Judgement Day", regretting not telling her that she always thought her a snappy dresser is a sad moment.
"Judgment Day" - Jenny may have had her issues, but Tony's reaction to her death, and his intense guilt over not tailing her, is absolutely heartbreaking.
The ending of "Corporal Punishment."
In a rather weird way, a good deal of "Dog Tags," at least if you happen to be McGee. Sure, it eventually turns out that the dog was framed, not to mention secretly injured, but it's kind of shocking to see Abby garner absolutely no sympathy for him, despite the fact he was nearly killed by a dog, and his injuries are clearly visible. Kind of sad, considering they've known each other for so long, and are very good friends.
The end of "In The Zone", where we find out that Nikki's brother Eric is alive, but in a coma that he has presumably never woken up from since he was wounded. Nikki just talks to him as normal, saying how happy Jamal's family was to hear he's doing well...
"Requiem" leaves you in tears from the moment when the team figures out that Maddie was Kelly's best friend.
Gibbs' repeated flashbacks of his daughter begging him not to go (this was presumably the last time he saw her before she was killed). At the end during his near-death experience, he now sees her telling him, "It's okay, Daddy. Go back.", essentially easing his long-held guilt over not being there to protect her.
Tony's frantic pleas for Gibbs to wake up, his voice almost cracking at one point.
The end of "Family", when Tony finally lets his dreams of a life with Jeanne go. Also a double Heartwarming Moment, one for the series in general (the parents reunited with their child) and another for Tony and the team showing just how much of a family they've come to be.
The last ten minutes or so of the season 6 episode "Dagger". Lee ends up sacrificing herself so Gibbs could kill the man who was blackmailing her. Then we find out that this was probably the best outcome for her, as the alternative was life in prison and never being able to see her sister again. Then Gibbs breaks the news to Lee's sister at the end of the episode as he hands her Lee's badge.
The look on Gibbs' face right before he shoots her is wrenching.
At the end of "Silent Night", when Gibbs convinces a man who has been absent from his daughter's life for nearly two decades to reunite by saying that he would give anything to hug his murdered daughter one more time.
When we learn Gibbs gets his "rules" not from his father, but via flashback from the first time he talked with Shannon.
An understated one in The season 6 episode "Collateral Damage". Gibbs is arguing with Vance about being assigned a rookie, and that he chooses his own damn team. Vance replies "Like you chose Agent Langer?", the agent killed in the season six premiere. The Tear Jerker part: Langer was framed, but they don't know that. Sure, he wasn't the nicest guy around, but he's remembered as a traitor instead of a man who trusted the wrong person. It's a good thing Gibbs got suspicious...
Agent Lee's sobbing in Gibbs' arms in the season 6 premiere. Made ten thousand times worse when you realize she's not only sobbing because she killed a man, but because she know he's innocent and she only killed him to keep her cover. She probably feels like absolute shit as Gibbs comforts her.
The end of season six. When Tony's sitting in the squadroom without Ziva, trying to explain to Abby and McGee that it wasn't Gibbs or Vance who made Ziva stay in Israel ...it was Ziva herself. Made much worse by how we know that Gibbs believes she's been lying to him, Tony believes she hates him and Ziva herself thinks Gibbs doesn't want her there... and then we switch to the scene of Ziva tied to a chair in Somalia, her face bruised and bloody.
Tony: Boss? One short?
"Broken Bird": Ducky is forced to face a monster who psychologically tortured him years ago while he served as a doctor in an Afghan refugee camp. But what brought it home was the very end when Ducky returns to work, quieter than ever before, and proceeds to break down in his girlfriend Jordan's arms.
The Season 7 premiere. They saved Ziva! She's back home, on the team! ...But see at how terrible she looks...
And the climax. Though it's sweet to see she's as concerned for McGee and even Tony as she's ever been on being reunited, her dialogue from the last few months screams Unwanted Rescue. Whatever torture she went through, compounded with Gibbs abandoning her back in "Aliyah," Ziva clearly does not expect to leave Somalia alive.Thankfully, Team Gibbs didn't come totally unprepared, making her ensuing rescue all the more awesome and heartwarming.
In "Flesh And Blood", Prince Sharif is chauvinistic, spoiled and willfully ignorant of the danger he's in. But at the end of the episode, when he is told that it's his brother who tried to kill him, the look on his face will make you want to hug him.
The end of "Borderland", where Abby discovers evidence of Gibbs' shooting of the drug dealer who killed his family. She comes to Gibbs' basement, torn up over what to do. This conversation happens:
Abby: Tell me how much I've been like a daughter to you, and how much you love me... Gibbs: Will that help? Abby: (Visibly struggling for control) No... What I really need to know, Gibbs, is if you're gonna love me, no matter what. (Grey-out, credits.)
The ending of the episode "Obsession," where Tony starts getting emotionally involved in finding an Intrepid Reporter who disappeared around the same time her Marine brother was killed by an old KGB-issued poison that was injected into his body, and which has been injected into the woman's body as well, and for which there is no cure. Throughout the episode, Tony finds himself getting more and more connected to the woman, and then eventually he does find her...only, they can't get together after all since she doesn't have much longer to live after having been injected with said poison. The final scene sees Tony going down into Gibbs' basement and having this conversation:
Gibbs: How did it go? Tony:She went peacefully. Gibbs:(Pause) You okay? Tony: Not really. (Sits down.) (Gibbs pours a drink and hands it to Tony, who downs it.) Tony: I broke Rule #10. Again. "Never get personally involved in a case." Gibbs:(Sympathetic) Yeah. It's the rule I always had the most trouble with.
What brings it home is when Gibbs asks if Tony is all right, and Tony whispers, "Not really." The way he says it tells you everything: he's past the point of breaking down crying; he's broken.
The Christmas present McGee helps give to the nephew of one of Abby's friends at the end of the episode "Faith". The little boy's mother is in the Navy and currently stationed overseas onboard a destroyer. McGee sneaks the little boy into MTAC where he has arranged for a video feed with the mother's ship. The look of surprise and delight on the faces of both mother and son when they see each other for the first time in months.
All through "Double Identity," people start wondering about Ducky's odd behavior, including his switch from wearing bow ties to neck ties. Near the end of the episode, Abby learns what has happened: Ducky's mother has passed away. Ducky takes it in stride, later reassuring Gibbs that it was her time to go: she had led a full life, she was almost 100 years old, and in her last few years, dementia had robbed her of most of the quality of life. Still, Ducky loved his mother and will miss her, and when Abby hugs Ducky at the cemetery... damn, I've got Sand In My Eyes.
Then the elevator doors open and we find Abby and McGee in an identical position. Tony extends his hand out to them, simply saying, "Bring it in" and they join him and Ziva for a group hug.
"Recruited" has a few, especially when it's revealed that the murdered Petty Officer was helping the boy to deal with bullying.
An especially heartwrenching one is The Reveal: the boy's father thought the Petty Officer was a sexual predator and killed him for it, trying to protect his son.
Doctor Magnus being reminded of all the people he helped.
Diane telling Gibbs, "You were my Shannon." It suddenly hits Gibbs just how much he hurt this woman by never opening up to her, and it kills him.
The beginning of "Engaged, Part 1", where Gibbs dreams about waking up next to Shannon as if nothing had happened. He looks so damn happy...
His expression and the gasp he lets out when he wakes up for real.
"Engaged, Part 2". Gibbs' flashbacks of the female recruit he had a crush on. The fact that he's still affected by her death indicating that he may have loved her just as much as Shannon.
Pretty much all of "Life Before His Eyes" with virtually every alternate scenario being a Cruel Twist Ending that had Gibbs, et.al being just as miserable as they were in the original. Even the ostensibly happiest one of Kate and Tony marrying and having a son has Ziva becoming a terrorist because she never joined NCIS.. Especially when Gibbs talks to Shannon and Kelly, with the revelation that he would have been killed had they not been is wrenching. The guy has spent years mourning them, no doubt assuming that they would have been blissfully happy had they survived, only to find out that the alternate was just as sad. . .
The small bit where he sees the younger version of himself kissing the female recruit he had a crush on. Even after all this time, even with the bliss he had with Shannon and Kelly, part of him still wonders What Could Have Been with this other girl.
In "Rekindled", Tony and the arson investigator, Jason King, instantly recognize each other when they hear their names. Tony is extremely uncomfortable being around Jason, and Jason isn't too happy to see Tony and holds a grudge against him for an unspecified incident with his sister. When the others probe, Tony reveals that twenty years ago, when in Baltimore for a Final Four game, he was taking a walk trying to clear his head when he saw a townhouse being consumed by an arson fire and heard Jason, who was nine years old at the time, calling for help. Tony managed to free Jason from his room, but then he heard Jason's four-year-old sister Amy trapped in her room. Tony tried to get there to save her, but the burning infrastructure and the wires that fell from the ceiling blocked the door and the fire was getting even more out of control. At that point, Tony was forced to choose between saving Jason and leaving Amy there, hoping that the on-the-way fire department could save her instead, or risk all three of them dying trying to save Amy. Tony chose to grab Jason and run out of the house, and unfortunately, the fire department was too late to save Amy. The flashback to Jason begging Tony to go back as they ran out makes it even worse, and you can tell Tony was NOT happy with being forced to abandon Amy. When Tony and Jason finally talk things out at the end of the episode, Tony makes it clear that there was nothing he could have done to save her and that night forced him to learn that he couldn't save everybody.
What makes this even worse is that Jason reveals to Abby that the cops and the fire department never found out who the arsonist was. So while he chose to be an arson investigator because he wanted to help prevent people from suffering the same fate his little sister did, it's also possible Jason chose the profession because he wanted to find the perp himself and avenge Amy.
The ending of "Till Death Do Us Part". While the fates of Gibbs, Abby, McGee, Tony, and Ziva are up in the air, the finale of the entire episode comes on a beach, where the shock of NCIS HQ's bombing and their being dead from the attack causes Ducky to suffer a seemingly fatal heart attack. The final gray-out of the season occurs with a shot of Ducky laying on his side, convulsing in pain. Especially painful was the thought that "Oh, Ducky's heartbroken but at least he's safe—Oh holy shit, is he having a heart attack?"
Abby remembering how she couldn't return a little girl's teddy bear, or prevent her from being taken away from town by her hateful father after her mother's death in "Hit and Run" was just too sad.
At least this one ended with a beautiful Heartwarming Moment(the reading of a fortune cookie fortune that Abby gave Gibbs when they first met), which is a real relief for the first new episode after the double whammy of "Shabbat Shalom" and "Shiva."
Season 10, episode 2, "Recovery." Throughout the episode, Director Vance is clipped and abrasive to everyone we see him interact with, but as he's psychologically evaluated by Dr. Wolfe, he reveals how much he wants to go back in time to stop the HQ bombing, the entire episode showing him trying to reassert control and enforce normalcy again. The real kicker is how much he blames himself for the bombing, pointing out how vulnerable he was, or what if he had his kids with him when the carbomb went off, barely holding back tears.
In the end of the season 10 episode "Shabbat Shalom", Ziva, normally the most reserved member of the cast after Gibbs, screams and breaks down into a weeping mess when she sees that her father has been shot to death by an assassin. This was after she was going to turn him in for murder too. This was the woman who shot her own brother and only uttered a quiet, but sad, prayer afterward. Seeing her in such a state for the first time in eight years is just heartbreaking.
Pretty much all of the last ten minutes of "Shabbat Shalom" qualify. By the time the episode finally ends - with Vance telling Gibbs that his wife has died in surgery - most viewers will just be beyond numb.
The look on Gibbs' face is positively wrenching, as you know he's not just sad for Vance, he knows all too well exactly what he's going through.
Not to mention the very last conversation Ziva has with her father. Eli spent the episode telling Ziva he wants to redeem himself, but realizes that his sins may be too great. Just as Ziva was starting to warm up to him, she spots evidence that he might have accidentally killed someone. When she confronts him about it, she reveals that he was right about his sins. In her last conversation with him, she told her father that he could never redeem himself in her eyes, which clearly breaks his heart.
Ziva: An innocent man is dead. You disposed of his body, and you lied about it. Eli: Yes, I did. But why is that the only part of this that you can see? Ziva:(With tears in her eyes) Because you were right. Your sins are too great. Eli:(Struggling to hold back tears) Ah. So be it. But will you please sit across from me at the dinner table one last time?
Dex the bomb-sniffing dog in "Seek" (10.18) is a walking Tear Jerker, from the beginning of the episode when he whimpers by the body of his handler, just killed by a sniper, to the end, when he takes a bullet his handler's murderer has fired at Gibbs and survives to retire with his handler's widow and attend his handler's funeral.
Tony: You know, I've been thinking about getting a dog.
Gibbs: That's not a dog. That's a Marine.
(episode concludes with a shot of Dex sitting at his handler's casket, paying his respects, and a dedication to all military dogs)
Abby's crisis of faith in "Hit and Run." After the events of the previous two-parter, and the case of the week bringing up memories of her first case, she's off her game, to the point of taking her first sick day ever. Seeing Abby absolutely broken is devastating.
McGee's empathy for her is as bad. It's obvious that he would do anything to help her, even though both realize that this isn't something he can fix.
The look on McGee's face when he hears that his estranged father is dying of stage 4 cancer is enough to break your heart. Even though it's clear that McGee has a very hard time even tolerating the Admiral, given years of abusive behavior, he still loves his father. Of course, finding out said information standing on the other side of a two way mirror while your father's being interrogated about his whereabouts in a murder case was probably one of the worst ways to hear the news.
This exchange in Ziva's final scene:
Ziva: Tony, you are so... Tony: ...handsome? Funny? Ziva: Loved. (Cue The Big Damn Kiss)
Tony begging her to come back and be with him, even if she doesn't come back to NCIS. And barely managing not to cry while doing so.
This quote: "Hardest 180 of my life."
Tony finding Ziva's star in his pocket on the flight back to the states.
Leroy Gibbs and his dad meeting up with Walter Back, the ex-Luffwaffe pilot who saved the latter's life in "Better Angel" by guiding him out of occupied airspace back to England. Without his help, both Gibbs wouldn't have existed. This episode was the last appearance of Jackson Gibbs prior to his portrayer, Ralph Waite, passing away. Which means that that meeting, with Jackson telling Walter that his son is "the best man I know" may very well have been the last day Gibbs spent with his father.
In "Devil's Triad", the head of the money laundering scam the team, the FBI, and the Secret Service is investigating kidnaps Emily, Fornell and Diane's daughter, as ransom for the money the team confiscated. While Emily is saved and the guy gets caught at the end, both Diane and Fornell, despite their constant arguments, are completely out of their minds with worry during the final quarter of the episode and are trying to comfort each other the best they can.
Jimmy's crushed look on his face and heartbroken tone of voice when he tells everyone that the woman who was carrying the child for him and his wife has decided to keep it. Questioning himself and wondering if he's really able to be a father can really hit home for anyone whose own attempts at adopting a child fell through.
Gibbs getting frustrated on how a Navy veteran in "Shooter" gets to be a homeless man in the end after being honorably discharged from military service. Even Vance hates that it happens a lot recently.
The Season 11 finale, saying goodbye to both Jackson Gibbs and his actor, Ralph Waite.
Gibbs' reaction upon being told that his father is dead. He just looks so. . . stricken.
The death of helo pilot Hannah Banks in "Twenty Klicks." Yeah, she was basically a Red Shirt, but a painful and lingering death is never a fun thing to deal with.
The B-Plot of "Shoot The Messenger"; Vance's doctor calls him and tells him he discovered spots on his lungs during his last routine physical. After consulting Ducky and a few other doctors, everybody thinks that he may have advanced lymphoma, but the only way they can know sure is if a lung biopsy takes place. Vance spends the whole episode pre-biopsy freaking out for understandable reasons. He lost his wife not too long ago; now he may die from a severe health crisis and he still has two underage kids. He even keeps both of them Locked Out of the Loop until he absolutely knows for sure what's going on so they don't have to worry about possibly losing the only parent they have left. Thankfully, at the end of the episode, it turns out that the spots are sarcoidosis, which is easily treatable.
A retired Marine in "The Searchers" tries his best to bring home the remains of his friend. Even though he died from being shot by a conman, NCIS was able to secure the remains in Da Nang.
The end of "House Rules," with McGee reading the letter he wrote to his father who died because he delayed the surgery that was his last hope of surviving cancer so he could spend one last Christmas with his family.
In "Check", after the death of Diane Sterling, Gibbs is in a total BSOD. Especially bad because the murder was deliberately staged to reenact Kate's death.
His flashbacks of her are wrenching and indicate that of all his post-Shannon marriages, this is the one that he truly regrets not working out.
Jimmy has one of his own, having reached his limit of what he can take in good humor. Ducky notes that he himself had reached that point long ago and that it's impossible to go back to how things used to be.
"The Lost Boys" has a lot of these.
After discovering a homegrown terror cell known as The Calling and unsuccessfully trying to talk a recent member out of bombing a city bus in "Troll," Gibbs comes across another new member, Luke Harris. For the next two episodes, including the finale, he has a few false starts with trying to connect with him throughout the episode, despite Vance, Teague, and a hallucination of Mike Franks warning him not to get sucked in.
Luke goes through a heck of a Trauma Conga Line, for a young teen. He was getting ridiculed at school for being an adopted Iraqi-American, so turned to The Calling for guidance despite the love and support from his adopted family. Then said family is found gunned down right after Gibbs successfully gets through to him, leaving him devastated and all but completely adrift.
"Dorneget didn't make it."
At the end, after Ned's body is repatriated, Gibbs hallucinates several deceased agents, including Jenny, Kate, and Mike.
Luke shooting Gibbs twice under Daniel Boone's orders, while Tony and Teague watch helplessly.
Luke expressing My God, What Have I Done? over supposedly killing Gibbs, enough to almost jump off a roof. Fortunately, Tony and Teague are able to convince him that Gibbs survived.
Basically, the end of "Day in Court" - Bishop's learned that Jake is having an affair, and as a result, decides to leave for Oklahoma for an indefinite amount of time. Playing "Say Something" by A Great Big World definitely adds to it.
When Bishop comes into the bullpen after Jake confesses to her about the affair, her eyes are red, clearly indicating shes been crying.
There's also the fact that's Jake's ruined his friendship with the team, all of whom clearly genuinely liked him but are now furious with him because of what he's done.
"Spinning Wheel". As Jake tearfully apologizes and pleads for a chance to save their marriage, Bishop sadly declares that their marriage is over and has been for a long time, otherwise he wouldn't have had the affair or told her about it in the first place.
In a flashback scene, Ducky being forcibly separated from his half-brother Nicholas.
In "Sister Cities", Abby prevents a plane from crashing into a city by hacking its GPS so that the autopilot makes it crash into an uninhabited forest. Then Gibbs gets a phone call from Agent Pride in New Orleans saying that Luca Scuito was on that plane. While it's eventually revealed that he wasn't actually on the plane, for ten eternal minutes it looks like Abby had just killed her little brother.
In "After Hours", McGee gets distracted by the anomalies in the current case they're investigating and violates the agreement that he and Delilah would only talk about work for one minute. Delilah gets angry with him at this, and then they end up fighting over it. After things calm down and the two of them talk it out, Delilah admits that she got so upset because she's scared about work becoming the basis of their relationship. Since the two of them are from different governmental agencies, there might be a time when they're not allowed to divulge anything to each other, and that's part of the reason why Ellie and Jake's marriage fell apart. This shows that Bishop and Team Gibbs weren't the only ones hurt by Jake's affair, and the whole thing has gotten Delilah worried about something similar happening between her and McGee.
In the end of "Scope", Gibbs chooses to sleep in his actual bed rather than his couch after who knows how long. Happy tears were shed.
In "Reasonable Doubt", DiNozzo Sr runs into a homeless woman who believes that he's her father. Over the course of the episode, it's revealed that she ran away from home because her real father rejected her for being gay, was suffering dementia, and had a brain tumor. At the end of the episode, she's taken to a hospital and her condition is diagnosed as terminal. DiNozzo Sr then walks into her room and plays along with her delusion so that she can die believing that she finally reconciled with the (long-deceased) father she hadn't spoken to in years.
When he says "I was angry. My wife died, I had to raise a child by myself, and I took it out on you. And I had no right to do that", you can tell that he was also apologizing to his son (who's watching all of this from the doorway) for his Parental Neglect after his mother died.
The end of the episode "Homefront". Fornell is shot multiple times and his fate is left uncertain as his phone rings.
This becomes even more of a Tear Jerker when you learn in the next episode that Trent Kort, a CIA agent he had previously worked with was responsible.
"Family First". Just "Family First". Ziva is Killed Offscreen by Trent Kort, leaving Tony grief-stricken throughout, as well as the rest of the team. Even moreso when Tony learns that Ziva left behind their daughter, whom he had never know about until now. And, finally, his decision to leave NCIS.
Gibbs teaming up with the son of the Marine killed trying to protect his wife and daughter. We've spent so much time focusing on the loss of Shannon and Kelly that we've completely forgotten that someone else lost a loved one in that accident too. He never outright tries to stop the guy, but warns him of what he knows only too well—avenging his father won't bring him back.
Alex Quinn's Freudian Excuse for her constant PTSD about Philadelphia, and leaving field work behind. She and her then-partner, Shaw were both on their phones while on a stakeout there. Shaw was telling her husband and young son she'd be late coming home, and Quinn herself was having a heated argument with her fiancee. When the former got out of the car to give Quinn privacy, a shoot-out ensued from the gang they were assigned to watch. Quinn, unable to save Shaw, was the only survivor.
To hammer it in, Shaw's phone call had still been on during the shooting. This meant her own family heard everything from the other end and there was nothing they could do.
In "Keep Going", the Victim of the Week's son, Ryan, blames himself for his father's death because he feels as if he wouldn't have been hit by that car if Ryan didn't need money due to being laid off the previous day. As a result, he climbs onto the ledge of a nearby building so he can throw himself off of it. Palmer is the first one of the NCIS team to notice Ryan on that ledge, rushes up there despite his fear of heights, and hangs onto him for the entire episode in order to talk him down. It makes Gibbs catching the road rager that killed Ryan's dad, and Palmer succeeding at convincing Ryan to keep living, all the sweeter.
While on the ledge, Ryan admits to Jimmy that he thought about commiting suicide before, but he never went through with it because he didn't want to break his father's heart.
Special mention to Jimmy's speeches on how he loves his job and his friends, and about looking for the good when bad things happen, especially since he sees a lot more dead bodies than the average person.
Qasim is shot to death.
The revelation that Bishop would have accepted his marriage proposal had he not been killed. Some Fridge Horror kicks in at the realization that this is the second tragic ending to a relationship of hers (her divorce being the first), and to make matters worse, it was the first she embarked on after her split.
The end of "A Bowl of Cherries" has Quinn's mother forced to accept the fact that she's coming down with Alzheimer's.
In "Something Blue," McGee's nervous breakdown after Delilah collapses under the pressure of their wedding preparations, and has to be hospitalized. Luckily, Gibbs talks him out of it and she turns out to be fine.
It's a small moment, but Vance's advice to Tim to enjoy every moment with Delilah and never take her for granted counts too— he loved and had a happy marriage with Jackie, a similarly "strong and intelligent woman," and clearly hasn't forgotten what happened back in Season 10.
The ending of "Rendezvous." Granted, everyone was under heavy fire from rebels, but when McGee stays behind in Paraguay to back up Gibbs, Torres looks back at the two of them with helplessness as he boards the last chopper.
The start of "House Divided" has seen Gibbs and McGee outgunned and captured after the cliffhanger of the previous season finale, and tortured for about two months, evident by the fact they've both grown full beards from captivity.
Some considerable Fridge Horror at one point when one of their captors bangs on their cell door with a baseball bat and Gibbs jumps back fearfully. Just how many beatings has he taken from that bat that he would react like that?
Tim's monologue about how much he misses his wife and unborn child. It even earns him the sympathy of one of the terrorists keeping him in captivity.
Despite successfully pulling off their Go Mad from the Isolation gambit to escape Paraguay, Tim admits to Gibbs, and Dr. Confalone that the real fear and worry he had to put aside for the last two months caught up with him, to the point that he's fighting perpetual anxiety and can't sleep.
It's revealed that Reeves goes to AA meetings although he refuses to actually talk. He gets close to Melissa, a woman who has just left her abusive boyfriend. Reeves sees her kidnapped and eventually hunts her down to where she's just killed her ex in self-defense. But the investigation eventually reveals Melissa set this whole thing up as she found her boyfriend cheating on her, killed him and was planning to sell secrets from his laptop. Reeves is naturally hurt when he confronts her but the kicker is when he sniffs her drink, discovers it's a rum with coke and realizes Melissa was faking being an alcoholic just to join the AA group. It drives him to a meeting where he starts to confess his own story of childhood abuse, clearly affected having bought the woman's con.
During a case, Gibbs discovers that Fornell falsified evidence to get Hicks convicted of a serial murder. Fornell defends it on Hicks being guilty but Gibbs points out the evidence shows the murder was committed by a left-handed person and Hicks is right-handed. On the stand, Gibbs is forced to testify about what Fornell did and the man ends up losing his job with the FBI and a clear break in their long friendship.
But the true tragedy comes when Hicks makes a slip of the tongue that makes Gibbs suspicious. He and Sloane check him out at a batting cage...and see Hick is a switch hitter, meaning he did commit the murder and Gibbs ruined Fornell's career for nothing.
This comes up later as Fornell is now a P.I. and Gibbs has been refusing to talk to him as he can't handle the guilt over telling Fornell what he did. When he does, Fornell is hurt...not because of what happened but Gibbs not telling him sooner so they could work together to bring Hicks down.
The shocking cliffhanger at the end of "One Step Forward", one of the show's biggest and most painful. For the first time in the series, and right before her departure from NCIS headquarters, Abby has been gravely wounded and lies in critical condition. One of the most beloved characters in the show, period, has been struck down at the last minute. And for the first time, Gibbs has failed to protect her. If there was ever a time for writers to inflict the biggest Gut Punch, then it was now.
And as a result, Clayton Reeves is killed in the attack protecting her. As a result, Abby leaves to honor the debt. It was known that Abby was leaving, but Reeves dying was a shock as well.
Gibbs laying flowers on Shannon's grave and wishing her "Happy Birthday".
Sloane's entire backstory, period. Held by the Taliban for nine months in Afghanistan, tortured, forced to choose which of her squad would die next... and the whole thing left her with a lattice of serious scarring across her back, a constant reminder of what she's been through. Seeing the usually-sunny Team Mom so desperate and hurting is.... ouch. Ouch.
"What Child Is This":
When we learn why Kasie felt such a close connection to the Victim of the Week. During Christmas the last year, Kaise and her dad got into a fight because she wasn't sure if she wanted to finish grad school, making him accuse her of not applying herself. Then a month later, he had a sudden and fatal heart attack on his mail route. The day after the funeral, she went back to Grad School, then a week later, she started working for Ducky, which to her proved that her dad was right.
The single mother, Tanya; she was a pregnant drug user who was disowned by her parents and abandoned by her boyfriend. While selling her baby to the drug dealer was wrong, it's hard not to feel bad for her for it.
In "Crossing the Line", Max, one of the high school interns, turns out to be the son of one of the agents killed in the NCIS bombing at the end of Season 9. He was also there the day the bombing happened, and is clearly suffering from Survivor's Guilt. When Max asks Torres why he survived and his father didn't, Nick admits that his father abandoned him and his family when he was little, and that he's still waiting for an answer for why he did that. Then Nick says that all the two of them can do is choose how they're shaped by their tragedies.
In "Perennial," Sloane's daughter, who she gave up at birth, refusing to have anything to do with her.