* Sam Fisher discovers files in Nikoladze's office that tell about the invasion he's conducting in Azerbaijan, with [[WarIsHell massacres of civilians]].
* The Police Station mission, where your mission is to investigate the morgue for the missing agents. In another part of the station we see a mercenary tortured to death and left to rot from his interrogation; apparently this kind of cruelty is not uncommon among these guys.
* Grinko himself, a former Spetsnaz officer who his personal driver mentions will gladly murder him if he steps out of line.
* The Abattoir mission. American and Chinese hostages facing execution at any moment, with Sam Fisher as their only hope.
* The ParanoiaFuel of knowing Nikoladze plans to detonate a [[https://en.wikipedia.org/wiki/Dirty_bomb dirty bomb]] somewhere in the USA.
* The ParanoiaFuel of knowing that there are five smallpox canisters hidden throughout the United States and nobody knowing where they are, plus the fact that they could go off at any moment unless the BigBad resets them every 24 hours. The final mission of the game is particularly chilling for people who have been to Los Angeles International Airport and are familiar with how smallpox spreads. Had Soth's bomb gone off, the disease could have found its way to dozens of countries in a matter of hours.
-->'''Suhadi Sadono:''' The pox is under your child's pillow.
* When Hugo Lacerda's men torture [[spoiler: Bruce Morgenholt]], you can hear screaming and electrical crackling. What's arguably worse is the way his torturers describe what they were doing and how long they were doing it.
-->He hasn't been able to talk for an hour. His tongue is a lump of coal!
** Worse is if you wait and listen to the entire thing; Morgenholt will eventually stop pleading for his life and they'll continue to shock him even after he has expired. His torturer is especially unapologetic for it.
* Towards the end, you have to disable a total of 4 very hard to find bombs while [[spoiler: Shetland]] sends EliteMooks with to hunt you down. This wouldn't be so bad but you have a very limited amount of time to find the bombs and those guards are far more perceptive than average mooks. While you're in the act of disarming the bombs [[spoiler: Shetland]] will seemingly come out of nowhere and try to turn you to his side, [[NotSoDifferent citing your shared experiences and previous friendship]]. The scary thing is, he seems to know exactly where you are. And unlike his EliteMooks, he isn't wearing [[GogglesDoSomethingUnusual night vision goggles.]]
* While PrivateMilitaryContractors are a lot often made evil in fiction, the game does a ''very'' good job of making you question if Shetland is in on the conspiracy right up until the very last moment. How does he reveal himself to be a bad guy? When he [[YouHaveOutLivedYourUsefulness kills a 'loose thread']] whom he is lulling into a sense of false security with a katana. Sam sees all this happen via their larger-than-life shadows projected on the paper wall of a traditional Japanese home. It adds a sense of surrealism to the horrifying scene, since it makes it look like some sort of shadow puppet play. It's also totally unexpected, even ''if'' you've come to the conclusion that Shetland's a bad guy.
* The final levels where [[spoiler:Tom Reed's Third Echelon]] has used EMP's to damage much of Washington DC while trying to conduct a DayOfTheJackboot, especially in the street scenes.
* The scenes of the massacre inside the White House where the place is littered with the bodies of Secret Service agents. ''Every single one of them is dead''.
* Blacklist takes this up to eleven with one of the largest US military bases in Guam being burned to the ground effortlessly and a hostage having his throat slit in Iraq.
** The Blacklist attacks also count because of the things the attacks target such as transport and utilities, their ability to be sped up if one is stopped, the large scale damage they can do and their sophistication and worst of all, the fact that they're highly plausible.
*** After Sam stops the American Consumption attack where the Engineers targeted Chicago's water supply, the news reports state that 2 million people would have been killed if it had been successful. American Freedom takes this up to eleven with VX nerve agent dispersal units being placed through Philadelphia's train network. To put this into perspective, without the proper protection, VX, one of the deadliest chemical weapons in existence, causes instant death to anyone exposed. [[spoiler:And then American Fuel ''succeeds'' in targeting the U.S.'s vulnerable coastal refineries, nearly setting fire to much of Louisiana and resulting in gas rocketing up to ''seven dollars a gallon.'']]
* The Engineers are also NightmareFuel themselves . They are the most sophisticated terrorist organisation in the world with capabilities that make them a NGOSuperpower. This is seen when they deal a devastating CurbStompBattle to the legendary Delta Force when the latter tries to storm their training camps in Iraq.
* The torture of [[spoiler:the Secretary of Defense]]. His subsequent NeckSnap could almost be considered a MercyKill as well as a ShootTheDog.
* [[spoiler:Kestrel]] when he is discovered the end of the co-op arc. [[spoiler:If his own agency, Voron]] considers an [[FateWorseThanDeath induced coma as imprisonment]], it's a bit of FridgeHorror when [[spoiler:Reed]] back in ''Convictions'' authorises the use of drugs to interrogate Sam. Would he have suffered a similar fate had [[spoiler:Anna not been working against Reed]]?
* Majid Sadiq is very unsettling. Sadiq's voice actor, Carlo Rota does an excellent job making him sound like an affably evil British gentlemen, willing to kill and torture innocent people without a second thought. His character also subverts the stereotypes that many Westerners hold towards Arabic terrorists. Yes, he is Arabic, and HELL yes he is a terrorist, but his motives are far more sophisticated than some Jihadist zealot, though no less radical. His accent and mannerisms evoke a sense of familiarity in a very scary way. But the worst thing about him is his competence. In previous games, Sam and his friends were able to outwit and destroy most of the opposition against them. Sadiq, on the other hand, with his [[spoiler: experience as a [=MI6=] officer]] manages to stay one step ahead, nearly killing Sam several times during the game and dreams up several very plausible and properly horrifying terrorist attacks which he nearly manages to implement.