A young, anxious, unnamed quokka checks in for their first day working on the Mirage Express, a luxury train created to host various events, including murder mysteries. They talk with the train’s good-natured conductor, who reveals that he's retiring after 32 years on the rails and planning on vacationing with his wife. The conductor briefs the employee on the train and on their role as an employee of the luxurious dining car; this consists solely of operating of the microwave, as the train possesses extremely advanced technology and has many robotic hands which carry out automated tasks for guests. After the briefing, the day’s party arrives for their murder mystery. The party: various friends and acquaintances of Sonic the Hedgehog, including the blue blur himself, who are celebrating Amy Rose's birthday party. The conductor and the employee take their tickets, and the employee is slightly anxious, due to the guests' celebrity and fame, as well as their various idiosyncrasies. The conductor heads off to the front of the train, and Amy sends each of her friends off to their respective rooms to play their respective roles, while she and Miles "Tails" Prower, who were given investigative roles as a journalist and a detective and thus can't be the murderers themselves, remain in the dining car with the employee. Suddenly, the train accelerates, and all three are knocked unconscious in the ruckus.
They awaken in the closet of the dining car, having gotten thrown back by the train, and discover that the door is jammed shut. Tails and the employee notice that Amy is acting awkwardly, and decide to practice for the mystery by investigating their current situation and following Sonic's example in their investigations, asking themselves "What would Sonic do?" They investigate the room and discover that Amy is embarrassed because, being the first of them to wake up, she attempted to use her Piko-Piko Hammer to break out while the other two were unconscious, only for the hammer itself to break because it was one of her weaker backup hammers (the employee is later confused as to why she had her hammer in the first place, as the train has a no-weapons policy and its automated system should have taken it; she explains that, as the birthday girl, she was given privileges, one of which is a dispensation for her trademark mallet). Tails repairs the hammer, and directs Amy to a weak spot to attack, clearing the way and opening the door. However, when the three re-enter the dining car, they see a startling sight:
Sonic the Hedgehog is dead.
Or at least, he’s the murder mystery’s victim, lying seemingly unconscious on the floor of the dining car. Tails and Amy praise him for getting into the spirit of the game by pretending to be hurt, and they race off to solve the mystery, with the employee close behind. However, the employee, who hears Sonic groaning and softly mumbling, realizes that Sonic might not be acting. After recalling the conductor's message asking them to help ensure the guests have a good experience and solve any problems, the employee resolves to help solve the mystery, and find out how Sonic can be helped if it is serious. They set off, ready to help solve The Murder of Sonic the Hedgehog.
They catch up with Tails in the next car on— an Old West saloon, host to Knuckles the Echidna playing the part of sheriff. However, he proves cagey and refuses to divulge what he’s been doing. The two investigate, and determine that, based on the lipstick on a glass and the damage done to a Super Monkey Ball arcade machine, and no thanks to the fact that the employee's hunch that there had to be a clue in a trash bin, Knuckles had been goofing off and not participating in the mystery. Sheepishly, Knuckles admits that he had been spending most of his time playing Super Monkey Ball with Vector the Crocodile and damaged the machine in rage when he couldn’t beat Vector's score. He also divulges that Rouge the Bat came through looking for something, and that Shadow the Hedgehog came through (though he stopped to teach Knuckles and Vector how to play Super Monkey Ball in the first place, surprisingly; he has the highest score on the machine, as well) and locked the door when he left. Knuckles unlocks the door and sends the two on their way.
The next car is a library, where Vector and his ninja friend and fellow Chaotix member Espio the Chameleon are resting. Vector, a butcher, states that his alibi is that he was in the saloon with Knuckles, while Espio, a poet, claims that he had been reading and saw Rouge come through and take a brochure, despite Shadow having come through the room and not seen Espio in it. They investigate and, based on the fact that a manual on the Mirage Saloon had been left out of alphabetical order, that Espio did remember the contents of the book, and again, no thanks to the lack of evidence inside the room’s trash bin, the two decide to accept the Chaotix's alibis, heading off to the next room.
The room after that is a casino, where Rouge the Bat, a business tycoon, and Blaze the Cat, a titan of industry, are situated. Tails interrogates Rouge on her traveling through the train, and she reveals that she's been searching for a blueprint of the train, as the casino's vault is said to hold a treasure which she has been searching for: a Fabergé Chao Egg. The two convince Tails and the employee to plan and aid them in their heist, only for the egg to begin suspiciously ticking when they arrive in the vaults and claim their prize. The four believe it to be a bomb and panic, trying various methods to prevent it from exploding; however, the employee inadvertently stumbles upon the solution by suggesting that it isn’t a bomb, as when it finishes ticking, it opens to reveal a bejeweled Chao necklace. Rouge takes it for her own, and after finding yet another empty trash bin, the employee and Tails set out again.
The next room is a lounge, with jazz music being played by a band of Chao. In there, the employee and Tails find Amy, who'd been ahead of them for most of the mystery (another concession of her being the birthday girl is that she got a skeleton key that allows her to access each of the different rooms without needing each individual door unlocked by whoever is in them); she's bragging to Shadow, who's acting even more guarded and brooding than usual, that she has bombshell evidence from an unnamed source which will solve the mystery. Tails and the employee investigate again and find two unusual pieces of evidence. The first is that a wardrobe has a secret door in the back leading directly into the library; the second that, for the first time, a trash bin does hold evidence, a printed screenshot of a ticket website showing a concert by Amy's favorite band, stuck under a desk holding a computer and a printer. Amy says that her source claims that Shadow, a locksmith, was the murderer, having taken out Sonic, dragged him through the secret passage to the dining car, and then used his role to prevent Amy from reaching the lounge. However, he claims that that is false, and after some prodding by Tails and the employee, he reveals why he's been locking doors and acting cagey: having forgotten to get Amy a present, he attempted to use the computer to get Amy concert tickets for her birthday, and locked the doors to buy himself some time. However, he didn't take into account that Amy can bypass his locked doors with her Birthday Key. Amy forgives him, and Shadow uses his last key to unlock the door to the last car, accompanying the three inside as well.
The final car is the conductor’s car, where Sonic, the captain, was supposed to be stationed. Inside, the group finds signs of a struggle, with a robotic arm ripped off its rail, a blow dart, a vent on the ceiling, and to everyone's disappointment (even Shadow's), no evidence in the trash can (the employee even initially decided not to look, wanting to end on a high note). Tails and the employee decide that they have enough evidence to prove who the murderer is and call everybody else in, though Sonic is nowhere to be seen, so Amy and Vector leave to get him (with Amy assuming that Sonic decided to take advantage of his role as the murder victim and get in a nap). The friends discuss how much fun they’ve been having, only for the fun to suddenly be cut short by a blood-curdling scream from Amy that reverberates through the train. The pink hedgehog re-enters the room alongside Vector, her expression carrying extreme concern for good reason: Vector is carrying Sonic, who looks genuinely unconscious, in his arms. Amy is enraged that one of her friends would go so far as to legitimately hurt Sonic and demands to know who did it. After reviewing the evidence, Tails and the employee announce that the killer was Espio, who had not been accounted for by anybody else, and whose encyclopedic recollection of the manual was to throw the investigators off his trail. They deduce that he had used the blow dart to knock Sonic unconscious, pulled the hand off its rail in the vent, used it to send Sonic to the dining car, and then used the wardrobe to bypass the locked doors without alerting Shadow, who he'd pointed the finger at as Amy's formerly-unnamed source. As they make the definitive accusation, Sonic recovers consciousness and confirms that Espio had been the one to take him out. However, he reveals that what actually happened was even worse than his attack and that they're all in grave danger, as he had made a startling discovery prior to being knocked out:
The train is a Badnik.
Sonic recounts his experience: he'd been talking with the conductor on how the train operated and wished to know what the power source was; they then found out that the train was being powered by a Flicky. Espio then took advantage of Sonic being distracted to hit him with the blow dart, which held a non-lethal sleeping agent, and disappeared before Sonic could explain anything. Sonic then tried to stay conscious and fight back as the arms descended on him and the conductor, managing to knock one off. However, the arms proved to be stronger than the weakening Sonic, taking the elderly dog hostage and sending Sonic through the vent to the dining car, accelerating to cause chaos which would hide the battle from the others. Still furious, Amy demands to know why Espio would shoot Sonic with a blow dart and how he even managed to get it past the train’s no-weapons system. He explained that he was given the dart by the train itself and instructed to target Sonic, thinking it to be simply part of the game. Despite the unlikeliness, everyone comes to the conclusion that the train itself is the mastermind that tampered with their murder mystery game. In a fit of rage, Amy demands the train to show itself, leading to her attacking the train. Suddenly, the train goes into lockdown, revealing itself to be sentient, along with explaining its motives. It plans on delivering the crew to its master, the nefarious Dr. Eggman, at his base in order to get a wish granted from its creator: forcing the conductor to remain with it on the railway forever. It accelerates again, knocking everybody out and throwing them into different cars.
Sonic and the employee come to in the dining car, and soon enough, Dr. Eggman himself appears via video screen. He reveals that he had converted the train into a Badnik as part of an entire line of trains to be used for transporting goods to his empire, and that the train is delivering Sonic and his friends for a reward, though he hadn't orchestrated— much less expected— this present turn of events. After taunting the two, Eggman signs off. The employee is left despondent, blaming themselves for the situation the party had fallen into, where Sonic's friends and allies have been captured because they hadn't spoken out about what they knew regarding Sonic's situation. However, Sonic snaps them out of their funk, ensuring them that it's OK and telling them to keep going in the face of negative thoughts, as what matters isn't causing a problem; it's making things right. Sonic asks the employee to help him save his friends and is inspired by the employee sharing that they had inspired themself by asking, "What would Sonic do?" Sonic blasts through the locked doors and fights through the train's defenses, rescuing his friends along the way. As they arrive in the conductor's car, Eggman mocks them again, and the train forces the conductor to utilize its controls against the heroes. Together, the gang faces off against the train itself, and they call it out for its selfish desire to force the conductor to stay with it forever. Espio plucks the Flicky out of the engine, Amy uses her hammer to knock the train offline, and Sonic catches her after the ensuing explosion. As the train powers down, it apologizes to the conductor, and the conductor solemnly sends off his friend. When the damaged train pulls into the station, the conductor and his wife embrace, ready to go on a vacation and bringing the train's Flicky with them. Sonic grabs a cake for Amy, and all the friends reaffirm their friendship as they wish Amy a happy birthday.
In his base, Eggman, who had been waiting to celebrate the train's arrival alongside his “kids” Metal Sonic and Sage, dejectedly realizes that the train isn’t coming and that Sonic had won yet again. He demands his lackeys Orbot and Cubot draw him a bath and shouts that it needs to have his angry rubber duck and not his happy one.
In a short epilogue, the employee explains that Eggman's alterations to the train system were later undone and recounts what they ended up doing after this experience, noting how, even if it was only for a day, they had crossed paths with some of the world's greatest heroes and helped them on a special day.
