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Nightmare Fuel: Thomas The Tank Engine
The very concept of scrapping engines is a pinnacle of Nightmare Fuel within the series. Consider that, at any time, you could simply be scrapped at the drop of a hat for not being "useful" enough. And in a universe of sapient engines, they are deathly afraid of the scrapyards, and for good reason.
In some background shots, there are pieces of scrapped trains and sometimes even whole, rusting bodies right there, to be seen by any engine passing the tracks.
Of course, this leads into Fridge Horror when you wonder just when an engine would die if they were scrapped. Originally, the impression was that when their fire is out, they are asleep/inactive, but this has been challenged and outright disproven by multiple episodes. So after seeing how much punishment a train can take through the various wrecks they're caught up in, just how much would it take to kill them? And would they still be alive during the process?
Diesel's growling in earlier episodes has been heard as a kind of audial Nightmare Fuel by younger audiences. It can still have such an effect, considering how Diesel acts so suave until something, like the Troublesome Trucks, frustrates him enough to bring his angry self to the surface.
Several episodes that feature train crashes and wrecks are quite unnerving. One early example is "The Flying Kipper" where Henry gets into that massive wreck after crashing into the breakvan of another train. The sudden strike, dark lighting, and the sight of Henry derailing are disturbing in their own right, with a dose of Tearjerker for seeing Henry in this state. And, as noted on the Fridge page, said breakvan had three guards in it. Only two are mentioned jumping clear of the wreck.
There's also the story of the Spiteful Breakvan. At the end, Douglas smashes through the Breakvan, splintering it to pieces. Granted, the Spiteful Breakvan is an Asshole Victim, but seeing a crane tote its face away is kinda unnerving.
Another Asshole Victim example would be S. C. Ruffey, the ringleader of the trucks in the yard that leads insulting songs against Oliver in "Toad Stands By". To settle with him, S. C. Ruffey is put at the head of Oliver's train so that he can bumped if he causes nonsense. S. C. Ruffey tells the rest of the trucks in the train to hold back, which turns out to be his fatal flaw. Effectively, Oliver pulls on S. C. Ruffey and tears him apart in Sodor's own version of Drawing and Quartering. Granted, he's put back together at the end of the episode.
It's worsened in the original books, where in both instances the two victims are heard begging and screaming in pain for the trucks to go forward, but to no response. Nothing gets in the way of the trucks' fun, not even the well being of their own kind.
The opening scene of "Percy's Ghostly Trick" where a spectral engine is seen coasting across the bridge at night, with some creepy music adding to the effect.
James easily has the nastiest angry face out of the main engines, simply because of how pissed off he looks. Then we have a brief scene in "Old Iron" where the camera is directly in front of the tracks where James rolls in unnervingly close with said angry expression glaring directly at the viewer.
Gordon's angry face is on the same boat as James'. The wrinkles on his forehead help make it look very unpleasant to look at.
A few of the engine's face masks look kind of creepy, due to a tad Uncanny Valley in their facial designs and expressions. Thomas and Percy's original "eyes closed tight" expressions stand out in particular (though it doesn't help they were almost always used as they were about to smash into something face first).
In the episode "Pop Goes the Diesel", Duck has a rather unnerving harlequin-like grin. One picture shows him with this same expression looking directly at the viewer. This has been dubbed his "rape face".
Speaking of said episode, there is one of the vans a big laughing rectangle face. The way it is hysterically laughing with its eyes closed looks as though it's scaring others in a haunted house.
There's also a nightmarish quality to the existence of the Troublesome Trucks/Freight Cars themselves. They giggle and take pleasure in engines' misfortunes, like to be a pain and interference, and are even willing to undergo their own destruction for the sake of getting back at an engine.
For example, look at the episode "Rusty Helps Peter Sam". The trucks being towed up the slate mine line try to warn the trucks going down that they're not going to crash into Sir Handel, their intended target, but Peter Sam. The downward trucks still snap their cables anyway and crash right into Peter Sam, who can only shut his eyes as the collision hits.
Smudger's fate. To clarify, he was an engine on Duke's old railway that was known for making a lot of spills and being careless. The manager "made Smudger useful" by essentially amputating him and transforming him into a generator that is supposedly behind the shed where Duke, Stuart and Falcon (the names of Peter Sam and Sir Handel then) were residing (even with a shot of a mournful Smudger trapped behind the shed). The railway closed down and while Duke was recovered, Smudger's fate is never disclosed.
What adds to this is the nature of what is done to Smudger. Imagine if Smudger was human. Basically, to "make him useful", they cut off his arms and legs and left him all alone and still functioning. Disproportionate Retribution much?
"Stepney Gets Lost" is an episode where, well, Stepney gets lost while going down the tracks at night. He comes across a disturbingly red glow and finds himself in the scrapyard. His driver and fireman go out to search for any help, leaving Stepney stranded on the line (and thus, completely unable to move). The diesels Iron 'Arry and Bert come up alongside and behind him, smirking at his situation while Bert pushes a helpless Stepney beneath a massive grabber with the intent of leaving him to be scrapped. And they take pleasure in this idea. If it hadn't been for the arrival of Sir Topham Hatt, poor Stepney might have been...lost forever.
Even worse? In this episode, Iron 'Arry and Bert are both Karma Houdinis. The effect is diluted due to Villain Decay in later episodes, but their first appearances here are frightening. The fact that they take pleasure in pushing a helpless engine towards a scrapping death...
They manage to revive this creepy quality in their later cameo in "Fergus Breaks the Rules". When Fergus ends up at the scrapyards, Iron 'Arry and Bert appear through the hellish red glow and ominously ask if Fergus "likes it there".
"Halloween" features Iron 'Arry and Bert trying to scare Thomas and Emily until the tables are turned after Emily is hit with a tarpaulin and scares 'Arry and Bert into thinking she's a ghost. At the end, 'Arry and Bert are punished while Thomas and Emily are essentially reminded that ghosts don't exist. At the very end of the episode (the UK version anyway), a small white ghost just happens to appear as Thomas goes away. Granted, it's a cheesy effect, but the fact that it comes out of nowhere at the very end, and emerges from the carcass of a scrapped engine no less, can give this effect.
One episode in the second season had Edward save Trevor the traction engine from scrap, and it proceeded towards a vicar buying him, and him and his children playing with Trevor on a farm. The closing line of the episode is written fairly harmless, and is simply Trevor falling asleep muttering the words "I like children" slowly to himself, over the thought of once again being surrounded by carefree optimism and fun. When watching it as a kid, it's harmless, but when you replay it as an adult, it kinda comes off creepy...
Boulder from "Rusty and the Boulder" really plays up Uncanny Valley. True, it's just a carved version of Gordon's displeased face mask, but seeing it fade is a tad creepy. So is the final shot of Boulder looming over the quarry where it zooms up to Boulder's frozen expression.
Boulder is creepy throughout the episode. Look at the damage it does. Look how close it came to running over several engines. One notable instance is when Rusty gets around the corner and believes he's safe, only for Boulder to somehow appear behind him.
The second season had a recurring Leitmotif for whenever an engine crashes. While it also qualifies as Awesome Music, the rising Jaws-esque riff gives a heavy sense of inevitable dread as you know something brutal is about to happen to the engine in question.
In the episode "Scaredy Engines", Duck ropes Thomas into staying at the Smelter's Yard to get back at him for teasing Percy. As soon as they exit the sheds, and suddenly we see the large door slam shut and Thomas is all alone and the scene itself is rather unsettling