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While the game is light-hearted and plays its murder mystery premise for laughs, there are some genuinely disturbing moments from time to time.
- The moment the train starts speeding up, the music changes to a track that is filled with a Drone of Dread, causing the player to get knocked out and wake up in the Dining Room's closet with Amy and Tails.
- The initial moment with Sonic's "murder" starts off shocking, though Amy gets over it fairly quickly, with both her and Tails believing that Sonic is just playing dead. When the player goes to inspect Sonic however, the latter passes out, leaving the player character wondering if his injuries are real or not. Tails tries assuring the player that Sonic really isn't hurt and is committed to the bit, even stating he takes naps in odd places, but the thought remains in the back of their mind. As it turns out, Sonic, after recovering for a few hours, truly was injured; he had discovered a dark truth about the train itself, and safe to say it wasn't happy.
- From Sonic's perspective: you've just learned your friends are in danger, and you're then shot with a tranq dart. Collapsing before you can warn them, you realize they think it's all still a game and walk right past you, neither tending to your injuries nor learning about the real threat.
- The Fabergé Chao Egg heist goes off without incident, up until Rouge turns the egg itself. Suddenly, the Bank Vault theme starts picking up pace, as the party realizes the Chao Egg is ticking. Panic ensues over the entire group, as they're about to set off a bomb. The moment is somewhat alleviated by Mood Whiplash of the numerous comedically wrong choices that can be used to stop it, along with the fact that it wasn't explosive at all, but it's possible to unnerve a player at first.
- The Conductor's Car starts with a somewhat unsettling track, not helped by the fact that the car is empty and the conductor himself is not present, with everyone realizing that they haven't seen him at all. This prompts Amy to call upon everyone to gather at the car, only to realize that Sonic hadn't arrived yet. As mentioned already, Sonic's "murder" wasn't just a bit and he really was injured.
- Once Amy realizes that Sonic was hurt, she becomes enraged at the thought of one of their friends taking things too far that they would cause actual harm to Sonic. Her Face Framed in Shadow portrait combined with her dialogue can be rather chilling as opposed to her typical Genki Girl personality.
- Once the true "murderer" has been revealed and Sonic has woken up from his blowdart-induced nap, he drops a big bombshell that changes the entire conceit of the story: the train is a Badnik, and a Flicky has been powering it the entire time. This is followed by the Mirage Express revealing itself to be sentient, and was the true orchestrator of the entire game. It manipulated Espio into poisoning Sonic with the blowdart, along with trapping the entire crew in it once the jig is up.
- Shortly after this reveal, its dialogue becomes rather possessive of the conductor, being a platonic Yandere for him, with the train intending to deliver Sonic and his friends to Dr. Eggman so its wish can be granted: to work with the conductor forever, as it doesn't want him to retire after working together for 32 years.
- Once the true nature of the Mirage Express has been revealed and the cast gets separated, the player and Sonic wake up in the Dining Car with the train's interior taking on an evil glow. It's at this time that Eggman then makes himself known, and reveals that he had converted several trains into Badniks, with some being designed to detect when the cast has boarded. It's a mystery to how long the doctor's managed this masquerade.
- Upon reaching the Conductor's Car again, the player character has the option to speculate on what Eggman has planned for themselves, Sonic and his friends. If you say "Please don't turn us into robots", Eggman replies that he'd consider that so Sage could have new playmates. For a simple Mythology Gag, it has horrifying implications if you think too hard about it. Not to mention this likely would've been the fate of the Player Character too, despite being a civilian who was just in the wrong place at the wrong time.
