"Missing". A story is told of a group of women that were smuggled out of the Philippines by Marines in order to continue their relationships in America. They were meant to go to the US, but the Marines' orders were changed so they went somewhere else. They starved to death inside the containers, and the lone survivor was so traumatized she began killing the Marines responsible.
The climax of " The Meat Puzzle". Ducky is Strapped to an Operating Table, gagged, and gets an IV needle inserted into his neck to make him bleed to death. The camera keeps cutting from Team Gibbs and their race against the clock to rescue Ducky to the sight of his blood flowing down a drain. Thankfully, they do save him in time, but one of the culprits decides that he can't handle going back to prison and slits his own throat while his mother screams in agonized horror.
Pictured on the right: The moment Caitlin got McLeaned on the show. A shocking headshot in the closing moments of the show with probably its most graphic scene to date at that time where a bullet tore through her head and a huge burst of blood ripped out. We later learn a grapefruit-size hole was made upon its exit. And Ari Haswari had done this simply to spite Gibbs, after meeting Kate in person and casually headshotting another woman.
The monster that is Kyle Boone. Especially when Team Gibbs finds the scrapbook filled with photos of his victims. And then his lawyer/partner in crime, when he kidnaps Paula Cassidy and gives her a To the Pain description of what he plans to do with her. And finally, we have Gibbs' parting line to Kyle right before his death date comes up. Short and savage.
"Boxed In". Tony and Ziva spend the episode trapped in a shipping container. Also in the container with them is a box of highly explosive and unstable cluster bombs. The kicker? Tony and Ziva are unaware of the presence of the bombs, leading to them unwitting endangering themselves multiple times through the episode as they try to escape the container. Even though the bomb is revealed to be a red herring, early scenes with Tony and Ziva in the container are still tense to watch.
In "Smoked", the utterly TERRIFYING Death Glare given by the killer once said killer's been caught. Scarier still, it comes from a womanSerial Killer who feigned innocence and forced Gibbs to warn Fornell (mind you, he says this in a stoic but very clearly freaked out tone of voice) to get away from her right then and there out of fear of what she could do the second a crack in the facade shows.
"Angel of Death" has a patient at Jeanne's hospital who died from a heroin bag rupturing inside him - he was a drug mule. His junkie sister and her boyfriend (who ran the drug op in the first place) show up to get the drugs before they're found. Near the end of the episode, the girl snorts heroin FROM HER DEAD BROTHER'S INTESTINE. Drugs mess you up, kids.
In "Sharif Returns", it's thoroughly disturbing to watch the normally badass Gibbs become increasingly disoriented to the point of madness thanks to the poison that's been slipped to him.
"Broken Bird". Ducky gets a switchblade shoved all the way through his hand, and the antagonist of the episode, Mr.Pain, is incapable of feeling pain, and used it to horrifying advantage by using Cold-Blooded Torture without sympathy. What makes this so scary is that he is missing his entire right eye, which is now just an empty socket as a result of having it carved out in the Middle East long ago, and the crazy bastard is okay with showing it to people sans eyepatch or the like, as a war trophy and an intimidation device.
Ziva getting captured in the Somalian Terroist Training Camp at the end of Season 6, we don't even get to properly see her face, but we do get to see her Star of David necklace get ripped off her, and her capturer asks her what she knows about NCIS...
"Kill Screen" starts out tame, with a petty crook at an event trying to pickpocket people with the classic bump-and-rob tactic. Then a cop on security detail catches him with a purse he stole and the guy has no good excuses to get him out of hot water. But then the cop looks into the purse, freaks the hell out, drops the purse, and draws his gun, screaming at the guy to put his hands in the air. When the purse hits the ground, a ton of fingertips and teeth spill out.And somebody was casually carrying this among a large crowd moments before it was stolen. Intermixed with Black Comedy.
In "Oil & Water" Agent Borin gives an extremely unnerving and graphic description of what it's like to be blown up.
More Adult Fear in "Homesick" when the children of military families suddenly come down with a mysterious illness. The fact that it happens during the Christmas season doesn't help at all.
Enfant Terrible Rachel Barnes in "Parental Guidance Suggested" - very creepy.
A woman is sent a death threat with the use of a dead rat in the car. Later on in the episode, Bishop and Quinn find a freezer full of dead rats.
Qasim Nasir's death. Right in front of poor Bishop.
Gibbs' and McGee's torture in "House Divided". Especially Gibbs'. There's 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?
The ending of "Burden of Proof". Gibbs and Jack campaigned against Fornell's testimony that a man could have killed someone on account of the fact the man is not right, but left-handed. Turns out the person they helped get off the hook for murder was ambidextrous.
Jack: Switch hitter... he played us...!
Abby's ruthless bluff that she poisoned King with cyanide in "Two Steps Back". It is by far the most cold-blooded thing she's ever done in her whole career, and proof that messing with her and killing the people she loves will bring out her inner demon.
Bear in mind, this is a woman who has almost two decades worth of forensic experience, knows chemistry like she's breathing air, and knows exactly how to avoid having a crime detected. Cyanide poisoning was a blessing, given she could have done pretty much anything to him, his drink or even the environment, and he may never have even known. The worst part, the entire possibility that the pill was a placebo, and she could have condemned him to a slow, agonizing death. It was the dawning realization on his face, as she tells him her play was made before she sat down that sells it. If she wanted him dead, he'd be dead.
Gibbs goes to check on Alejandro Hernandez in prison, suspecting him of ordering the hit on his teammates. After exchanging some spiteful banter, Gibbs firmly grabs hold of him by the collar, coldly and calmly threatening to KILL HIM if he finds out Alejandro has ANY involvement in this.
Season 15's finale. In what is a franchise-wide Cliffhanger where ALL THREE NCIS SHOWS leave us in the lurch on their season finales, this one actually has the most hopeful situation. Dr. Vance is kidnapped by a man pretending to be friendly and ambassadorial as long as it suits him... and then drops the act once he gets the chance to snatch the Director of NCIS, calling him an "infidel" in the same hateful tone of voice Jack dreaded hearing.