Nightmare Fuel / Thomas and the Magic Railroad

• Keith Scott, the original voice for Diesel 10, was apparently far too sinister for a children's film, so all the lines had to be redone without his Australian accent. Despite this, his face and giant claw are still terrifying.
• The scene of Diesel 10 sneaking up on Mr. Conductor and the engines, and attacking the sheds.
  • Soon after that, Diesel 10 finds Mr. Conductor again...without the sugar. He grabs him with Pinchy and drags him to the viaduct, threatening to drop him off if he doesn't tell where the magic buffers are. It's one of the few times in the entire franchise that we see an engine explicitly threaten a human's life. Not to mention that a combination of his weight and the lack of gold dust causes the viaduct to start crumbling to pieces. Mr. Conductor only barely manages to escape in time.
• The original cut featured P.T. Boomer, who was supposed to have been the show's first true human villain until he was scrapped from the film after test audiences thought him him to be too scary for children. Whilst his motives were supposed to have been extremely petty (pretty much being a lame prototype to Sailor John from Sodor's Legend of the Lost Treasure 15 years later) and the way that he ultimately went around accomplishing them could've been done more effectively, he was still supposed to have been shown in a very threatening light. A good portion of the film's original conflict focused on how his presence in Shining Time was completely out of place, with scenes like him deliberately crossing the railroad tracks seconds before the Rainbow Sun went through, how he planned on blowing up Muffle Mountain to get to Lady, and how Stacy feared what he could do to Mr. Conductor had he known of him. He also crossed the Moral Event Horizon by crashing Lady after threatening Brunett into driving her. And this was to have been done with human characters, not the models, giving his scenes far greater gravity. And think about it, almost all of the humans in the series have been portrayed as kind authority figures, but here, we get a human character whose only motives are pure undiluted destruction for the most petty of reasons.
  • The workprint finally shows Boomer off...and indeed, there are a few scenes with him that probably set off alarm bells for people:
    • His Establishing Character Moment, first by grabbing a box of explosives while glaring at Mutt, is rather intense, and then by rushing in front of the Rainbow Sun just before it goes through, continuing to glare at the train in the process. It helps establish that he's a very ominous and potentially violent character.
    • The scene where he creeps up behind Patch and offers to bribe him. While it might seem small potatoes compared to how willing Sailor John was to cause physical harm...it can set off stranger danger signs.
• While played for laughs, one early scene is quite scary: when Mr. Conductor is alone in Sir Topham Hatt's office, there is an Uncle Sam Wants You-style poster of Sir Hatt pointing and smiling. Mr. Conductor playfully tries on the top hat on the hat rack and goofs around in a deep voice... and then turns around only to see that Sir Hatt in the poster is now glaring. It changes from that to a different frown, and finally a small smile as Mr. Conductor puts the hat back. It was meant to be funny, but still...
• The scenes with the high-pitched, almost shriek-like sound of Lady's whistle around Muffle Mountain at night. Once you learn more about Lady, it becomes more of a Tear Jerker than NF, but when your first hear it, it can be downright chilling.
• Like the series at the time, the train faces can be mildly creepy for some, as explained in the Other folder of the Nightmare Fuel page of the main series. But when the humans and the trains are in the same scenes together, the Uncanny Valley-ness of the trains can increase tenfold just because of the juxtaposition.
• The scene where Diesel 10 has James and Junior cornered in the smelter's is TERRIFYING. If Junior hadn't managed to teleport both himself and James out of there, Diesel 10 would have probably KILLED them!
• After Diesel 10's assault on the Engine's Shed where Mr. Conductor is also staying, they all fall asleep eventually, but Mr. Conductor soon after begins to have a particularly haunting Nightmare Sequence in which he envisions a Bad Future where poor Stacy is wandering about a terribly wrecked, vandalized and utterly abandoned Shining Time Station that's blanketed in an ominous fog. In the nightmare, Stacy is shown calling out to Mr. Conductor and asking where he is and why he never returned to Shining Time or to The Isle of Sodor anymore to help, and she then despairs over how the magic is now all gone. The music that plays during this moment certainly doesn't help either, serving as a haunting Dark Reprise of Shining Time's Leitmotif from the beginning.
  Nightmare Stacy: (Distraught) Mr. C? Mr. C? Why aren't you here? Why couldn't you travel anymore to The Isle of Sodor, or back home here to us in Shining Time? The magic is all gone...(cries).
  Mr. Conductor: (Awakens suddenly with a gasp) Ah!
  • It also doesn't help that, very faintly, the sound of what could easily be taken as the ominous sounds of a storm, or perhaps even ghostly moans, can be heard echoing throughout the apocalyptic Shining Time Station, perhaps symbolizing the poor lost souls who suffered because of the potential destruction Diesel 10 will cause and even representing Mr. Conductor's fears of not being able to stop the destruction of Sodor in time.