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Nightmare Fuel: TRON: Uprising
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...
Pavel's "test run" of his restored upgrade disc in "Rendezvous". He gleefully 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. Faces are not supposed to do that.
Code worms (again from "Rendezvous"). Dear Users, code worms. They're essentially the Grid equivalent of 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).
In Dyson's flashback in "Scars, Part 1" at the gathering of Tron, Dyson, Clu and Flynn, Clu's Evil Twin tendencies are shown in a rather jarring way. He stands behind Flynn, emulating his movements, but unlike Flynn who smiles in a friendly and almost fatherly way, Clu's expression is a wicked Psychotic Smirk.