* ''Tron'', of all people, takes a turn for the terrifying in the "Scars" two-parter.
-->'''Tron:''' ''(to Dyson)'' You watched me die? ''I'll watch'' '''you''' ''die''.
** His facial scars expanding to their horrific full extent in response to his hatred helps quite a bit in this regard. Not to mention the fact how easily he attacks Beck, his supposed friend and successor.
** Dyson's own scars from when he was mutilated during the ISO riots were also quite horrific since most of his head and one of his eyes was torn off from the attack.
* The torture scene in Tron's backstory. It's mostly shown on screen, with Tron strapped to a table and Dyson just cutting away at him with a buzz-saw. When the camera changes to a shot of the guards right outside the lab, there are bright flashes of light visible through the door every time the buzz-saw revs up and cuts into Tron. Then he does it to Tron's face. Jeez...
* The Coliseum Games in general. Prisoners and lawbreakers are thrown in the Coliseum to die in various ways to entertain the cheering sadistic masses, such as harmless prisoners thrown against skilled fights in death match disc wars or being torn apart by light cycles. Citizens in Argon City all live in terror of being sent to the Coliseum, even the ones cheering when others are killed there. The worst part is you can get sent to the Coliseum for as something trivial as breaking curfew by losing track of the time as Rilo found out.
* Pavel's "test run" of his restored upgrade disc in "Rendezvous". He gleefully provokes and ''murders'' a group of prisoners. His smile just before is ''incredibly'' off-putting. To say nothing of his manic laughter and psychotic expression ''whilst'' he does it.
* Gorn at the end of the same episode. Pavel had her face paralyzed by messing with her code so she couldn't reveal his involvement in framing Paige.[[http://static.tvtropes.org/pmwiki/pub/images/gorn_tron_uprising_nightmare_fuel.jpg Faces are not supposed to do that.]]
* Code worms (again from "Rendezvous"). ''Dear Users'', code worms. They're essentially the Grid equivalent of [[Film/StarTrekIITheWrathOfKhan Ceti Eels]] (except they enter through a Program's ''eye sockets''), they can be used to implant false memories within a Program's code or disc or to delete real ones, and they can cause ''hideous'' physical damage to a Program when mishandled (a mishap with a code worm is implied to be responsible for the hole that obliterated one of Gorn's eyes and goes ''all the way through her head'').
* Some of the deaths in this show look like stuff out of a horror movie. For instance: [[{{Gorn}} A soldier bisected by the waist, dragging himself across the floor, while bleeding pixels all over the place]].
* In Dyson's flashback in "Scars, Part 1" at the gathering of Tron, Dyson, Clu and Flynn, Clu's EvilTwin tendencies are shown in a rather jarring way. He stands behind Flynn, [[UncannyValley emulating his movements]], but unlike Flynn who smiles in a friendly and almost fatherly way, Clu's expression is a wicked PsychoticSmirk.
* The [[SlasherSmile faces]] Cutler makes [[spoiler:as he dies.]]
* [[http://tron.wikia.com/wiki/Cyrus Oh my god, Cyrus!]] His debut episode and the NotQuiteDead at the end were appropriately creepy.
** Cyrus' {{Leitmotif}}, "Compressed Space". In invokes the claustrophobic feeling of what is to be trapped in a damp, cold, dark cell and GoMadFromTheIsolation, just like Cyrus did.
* The scene where Tesler recruits Paige. Not only is is creepy because Tesler is lying through his virtual teeth, but that the scene behind him is a ''hospital'' that's covered in patches of bright color - [[SymbolicBlood the remains of Paige's patients and co-workers]] that he just slaughtered. And even after all this virtual bloodbath, his voice is perfectly calm.