Despite being a whimsical story about a boy learning the importance of learning accompanied by the suave and energetic animation of Chuck Jones, the animated adaptation of The Phantom Tollbooth is filled with dark elements that manage to be even more disturbing than the book's already-grim ideas, and Jones is willing to go into much more terrifying designs for the villains than his usual comedic brand of characters.
- The soundtrack while very whimsical most of the time, always has an undertone of menace until the conflict is resolved, hinting at the darker elements of the story that become clearer by the time they reach the Mountain of Ignorance.
- Before the adventure even begins, Milo is confronted by a stark red and white striped box that clashes with his realistically muted room and it comes to life in as elements pop into existence in an instant as the boy is understandably freaked out.
- It then sends out a black platform as it starts to spin, gradually crafting the car out of nothingness.
- The physical map of the Land Beyond displays the Mountains of Ignorance as grotesque faces, hinting at the nightmarish creatures long before they appear.
- Officer Short Shrift, a vaguely human-like police officer who has a single wheel with an extending lever as a leg and a visor that completely obscures his eyes, which are only revealed when he takes on the role of a jailor, but also the entirety of his face aside from his mouth. He also has a habit of delivering disproportionate jail sentences of millions of years for the most menial offenses.
- The Doldrums, while not seemingly menacing, being a dreary place embodying the lack of will to do anything made of sludge and populated by the Lethargians. The personifications of Boredom, Sloth, and Lethargy, a race of lazy, yellow-eyed creatures made of a grayish, semi-transparent liquid-like substance that causes these race's individuals to combine and separate into copies or the same being, only having the interest of being lazy, but if on closer examination, their goals have insidious purposes. They will deliberately do their best to keep you where you are hiding their truly malign intentions under a relaxed and casual facade that hide their wicked true natures to rob victims who happen to get into the Doldrums of complete agency including breathing and thought until one dies or is assimilated into them as a dangerous alternative, but both choices are hinted at and never directly stated, making it even more frightening than if they made their end goal clear.. A particularly sinister moment comes when the laidback facade drops mid-song and the Lethargians start shooting devilishly triumphant looks at each other as their trap does its work on Milo. They also have a habit of having a distorted reverb to their voice as if the sound is slowly catching up to the words, which makes them even creepier.
- And it’s frighteningly easy to be directed there as just a small instance of obliviousness and laziness can cause one to be directed there by reality itself. If one ever loses focus for a moment, they are pulled into the realm and the trap of the Lethargians. Milo is heavily implied to be one of countless victims, and if Tock wasn't there to rescue him, Milo would've been subjected to whatever the Lethargians had in mind for Milo.
- And when Tock frightens them away, they redouble their efforts by gradually building up to a colossal wave meant to consume them.
- Compared to Chroma's gradual and elegant composition to turn the setting dusk into night, Milo's attempt of raising the sun starts off a bit off with the sunrise unnaturally rising before Milo flickers so stars off. He then goes too far when he causes the sun to collide with the moon, which causes the sun to pulsate and split into pieces into increasingly abstract shapes, followed by purple rain clouds, a series of rainbows against a black background before they condense and expand in a warped cycle, and concludes the sun and moon rise in increasingly deranged shapes. As Milo and his companions leave, the sky below the Mountains of Ignorance flickers between colors. Milo understandably feels guilty and it sets the transition from the whimsical first half to the darker finale.
- The Demons of Ignorance drawn in a very rough style compared to the lightly drawn cast, and many look very disturbing. After the heroes defeat the Gelationous Giant, the demons start to pop out as the heroes rush towards the Castle in the Air.
- The Two-Faced Hypocrite, which looks like a two-headed dragon with a deranged expression.
- There's also the Insufferable Know-It-All, a a blue-skinned obese humanoid with a long nose and yellow sclera eyes with red irises walking directly at the camera while chiding the heroes.
- The Horrible Hopping Hindsight who has legs arched backward, with pink bloodshot eyes in a perpetual elongated outside the socket while breathing fire, looking like something retroactively out of a Rob Zombie album cover than a simple children's story.
- The Gorgons of Hate and Malice look like demonic snails with the Hate being a green draconic creature while the purple one has a vaguely beak-mouthed face.
- The Threadbare Excuse who is interpreted as a palish yellow creature with a body that has enlarged hands/feet, elongated lower jaw/back of the head yet the joints for neck/arms are almost nonexistent. It almost seems to be in perpetual pain for just existing as he walks a slow zombie-like stride.
- The Gelatinous Giant's eerie, despair based suicide in contrast to its literature counterpart that was merely freaked out, by taking its gelatinous status literally by slowly melting away at the very thought of an idea. Not helped by the fact, its voice gets deeper and distorted as it bemoans its fear of change.
- The Terrible Trivium, a being with no visual face and in the movie, is essentially an animated suit given form with his head being the only indication of his humanoid nature, but his intent is what makes him a special kind of unnerving compared to the others. His seemingly polite nature to convince others to do menial tasks is accented with the capacity of suddenly gaining sinister indications of eyebrows and his slow approach to the heroes with a twinkling flash in the indication of where his eye should be during his Badass Boast implies he was going to do something terrible to them before Tock frightens him off.
- After the Trivium dies, the Demons get fed up and decide to gather together to form the personification of all Ignorance, a bluish-purple leonine-draconic hybrid made from the various demons of the worst evils of man combining together into the thing they all spring from: HATE. In it's brief appearance, it temporarily kills Tock and it would've smashed Milo and the Humbug as well, had Milo not used his trump card to kill it.
