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- Baccano!'s "Pussyfoot Express" plotline has several criminal plans clashing at each other, most of which occurs—wait for it—on a train.
- Detective Conan has more than one case settle in the train. Also an important arc called "Mystery Train".
- Fullmetal Alchemist has a terrorist attack inside a train in the early stories. Too bad for him that Ed and Al are on board.
- Soul Eater: episode 30 of the anime, "The Red Hot Runaway Express". Kid, Patty and Liz have to board the speeding train and fight an enemy on board for possession of a magical artifact, while a third party outside is fighting both sides.
- Joker Game episode 6 takes place on the Asia Express when a Soviet diplomat looking to defect from his country ends up murdered before he can make contact with D Agency spy Tazaki.
- The Sin City short story "Wrong Track" features a man who thinks he has gotten lucky by finding a lover on a train. It turns out, she is an assassin who snaps his neck and throws him off the train.
- One issue of The Tomb of Dracula had the Count doing his thing on a moving train. Coincidentally, the vampire killers after him are also on the train.
- Hitchcock's spy thriller The Lady Vanishes. A old lady who had befriend a young woman on a train vanishes. This added a psychological element because everybody else denies seeing the old woman and there's no apparent way they are all in a conspiracy. One them is a nun and two of them are English toffs who don't want to be held up and miss the cricket.
- The Gene Wilder- Richard Pryor film Silver Streak has Wilder's character see a man thrown from a train. The film doesn't stay on the train, in fact he meets Pryor's character off the train, but in that first stretch he gets set up for the crime which means that he gets isolated from society and has to get back onto the train to solve the issue himself.
- Transsiberrian takes the elements of this trope to the extreme. It's the longest train journey in the world against some of the most famously inhospitable territory involving Americans travelling from China to Moscow. In order to work in some believable chase and action sequences they don't stay on the same train but they stick to their guns and have them steal a section of train.
- The 1946 Sherlock Holmes film Terror By Night has the detective solving a case of murder and a theft of an priceless diamond in a train. The film was touted with the Tag Line "One Way Ticket To DEATH!"
- In Sherlock Holmes: A Game of Shadows, Watson and his wife are on a train for their honeymoon. However, Moriarty sends a number of henchmen dressed as British redcoats to attack them as a distraction for Holmes, who snuck onto the train earlier disguised as a woman and hid in the lavatory. Holmes throws Mary off the train deliberately before he and Watson manage to defeat Moriarty's men.
- The original Under Siege was a well known example of Die Hard On A Boat, so for Under Siege 2: Dark Territory they went for Die Hard On A Train.
- An alien from ancient times is set loose on a moving train in Horror Express (starring Christopher Lee, Peter Cushing and Telly Savalas).
- The Slasher Movie Terror Train has a killer extracting revenge on a train full of masked partiers.
- In Runaway Train, tension is building between a train operator and the two escaped convicts who hijacked the vessel made of four locomotives.
- James Bond:
- A significant portion near the end of From Russia with Love takes place in a train, where the The Dragon finally makes his move to kill James Bond.
- At the end of Live and Let Die, Bond battles the henchman Tee Hee before joining Solitaire in bed.
- The Spy Who Loved Me likely refers to FRWL with a similar scene of another Dragon, Jaws, trying to kill Bond and Anya Amasova.
- Spectre likely refers to all three films with yet another Dragon trying to do precisely the same thing.
- Snakes from a victim of a curse start attacking people on train onroute to L.A. in Snakes on a Train.
- Train, where the eponymous vehicle turns out to be operated by organ snatchers.
- The Cassandra Crossing: A terrorist breaks into a NATO lab in Geneva, accidentally infects himself with an artificial virus, and escapes on a transcontinental express train. A US General Ripper finds out about this incident and orders the train not only sealed but rerouted to Poland and dropped into a gorge, all thousand passengers aboard killed, and any evidence of this top-secret biological weapon outside the lab destroyed that way.
- The Narrow Margin (and its 1990 remake) has a woman who witnessed a mob hit hiding on a train, and hitmen searching for her.
- Shanghai Express involves Chinese rebel bandits waylaying a train and holding the passengers hostage.
- Murder on the Orient Express: Murder = thriller. The Orient Express = train. Bear in mind it comes from the same author who mastered the Nasty Party and uses it in much the same way for the purpose of subverting one of the big conventions of that trope.
- Another Agatha Christie work, The Mystery of the Blue Train: also deals with a homicide on board a train, though unlike Orient Express, the entire novel does not take place on the train. (It's an expanded and relocated version of "The Plymouth Express" in Poirot's Early Cases, which of course is another example.)
- 4.50 From Paddington: the story opens with Miss Marple's friend witnessing a murder on a train running next to hers, and the first mystery to be solved is why there is no body to be found on the train or even lying in ground near the tracks where it might have been thrown from the train.
- Short story "The Napoli Express" is Lord Darcy's version of Murder on the Orient Express.
- The Phryne Fisher novel Murder on the Ballarat Train, although only about a third of the novel is actually set on the train.
- Alexey Tolstoy's story The Beautiful Stranger is a spy thriller on the Express.
- James Bond
- A Nancy Drew/Hardy Boys Supermystery titled "Mystery Train" had the titular characters taking a cross-country train ride that inevitably turned into a Busman's Holiday when both a murder and an inexplicable disappearance occurred.
- Clockwork Century: Dreadnought is largely set on the eponymous train, with a mystery involving exactly what the Dreadnought's mysterious cargo is, and why so many people want it.
- The Benny Hill Show has a Murder on the Orient Express sketch once using various US TV detectives (Kojack, McCloud, etc.) along with Hercule Poirot (all played by Benny Hill).
- Chuck season 3, episode 14, Chuck vs. the Honeymooners. Chuck and Sarah are on a train and see an ETA member and try for an impromptu mission using the other passengers' items as gadgets.
- The Goodies parodied this trope in "Daylight Robbery on the Orient Express'', with the Goodies arranging a mystery on a train for a convention of famous detectives..
- The Murder, She Wrote move South by Southwest begins as a version of The Lady Vanishes, with Jessica on a train to El Paso.
- The episode "Murder Takes The Bus" has most of the trappings of a Thriller on the Express, only...
- On SCTV there was a parody sketch of Orient Express called "Death Takes No Holiday," featuring John Candy as Hercule Poirot uttering the immortal lines, "Someone abord zis train is a Murderer! — Perhaps even ze Train Itself ... IS A MURDERER!
- Call of Cthulhu supplements Fearful Passages ("The Iron Ghost" adventure) and Horror on the Orient Express both have train-based adventures.
- TSR's Top Secret, adventure TS005 Operation: Orient Express. A set of espionage adventures that occur on the famous title train.
- The Merc 2000 setting of Twilight 2000 had an adventure called "Mess on the Orient Express", which involves the player characters having to find a stolen giant Buddha on the Orient Express.
- The Last Express. The Pre- World War 1 Orient Express setting gives it a very Christie feel and then it actually tries to use some of the same setting advantages that you might get in other media using this trope by having the game take place in real time.
- Chapter 6 of Paper Mario: The Thousand-Year Door is a Breather Level that largely takes place on the luxuriant Excess Express. You get roped into solving a mystery that follows this formula during the three-day trip, and, except for a brief rest stop at an abandoned station, is totally devoid of actual fighting until the Traintop Boss Battle on the last day. It also averts the lack of security normally present in these stories—the train staff refuses to let Mario into restricted areas, let alone outside the train. The boss battle is on the traintop because the boss had already captured everyone on the train except the conductor, leaving an unobstructed path out.
- The Ecliptic Express level in Resident Evil 0 has zombies (naturally) and a giant scorpion onboard.
- The game Chase The Express/ Covert Ops Nuclear Dawn is sort of a clunky Metal Gear Follow the Leader set on a trans-European train that will launch a nuke when it reaches its destination - although unusually for this type of story, there are a few stages that take place on a different train running adjacent to the main one.
- The first part of Professor Layton and the Diabolical Box is set on the Molentary Express, theough the mystery is more about the train's destination than the train itself.
- The Ruby Gloom 2-parter "Last Train to Gloomsville" parodies just about every train-thriller cliche to the max.
- The Looney Tunes short Boston Quackie takes place on board 'Le Cloak and Dagger Express'.
- The King of the Hill episode "Strangeness on a Train" has Peggy set up her birthday party on a disco-themed murder mystery play on a train. When her streak of unlucky birthdays leads to the mystery getting spoilednote , Hank tries to cheer her up, which leads to their having sex in the bathroom. Kahn discovers the "evidence" and starts a new mystery to try and figure out who it was, as Hank and Peggy desperately try to prevent it.
- Danger Mouse On The Orient Express takes place on said train, where DM and Penfold must retrieve a document that would allow Baron Greenback to raze all of Europe's tourist attractions and lure tourists to his (shudder!) museum of Barry Manilow record sleeves.
- The Bugs Bunny cartoon Wild And Wooly Hare climaxes with Sam and Bugs playing chicken with trains.
- My Little Pony: Friendship Is Magic episode MMMystery on the Friendship Express is about an investigation into who ate the cake Pinkie Pie was guarding. Much spoofing of mystery tropes ensues.
- The Adventure Time episode "Mystery Train" plays it straight for the most part. ...but then subverts it at the last minute, by making the whole thing an elaborate birthday prank/staged mystery put together by Jake for Finn's birthday.