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A reproduction of the Orient Express was built that travelled in space along hyperspace ribbons. It attempted to recreate the land-based Orient Express down to the fine details, with some omissions. (TV: Mummy on the Orient Express)
The Eleventh Doctor received a call requesting his presence as it was having trouble with an "Egyptian Goddess" who had escaped from the Seventh Obelisk. (TV: The Big Bang)
Eventually the Twelfth Doctor heeded the request, confessing to Clara Oswald that he knew they were being lured into a trap. He confessed to Clara that the Express' computer Gus had "tried to entice" the Doctor into coming there several times before through free tickets and mysterious summons, and that he "even phoned the TARDIS number".
The Foretold, a mythical mummy, was on board and murdering passengers. The Doctor soon deduced that all the passengers on the train were experts and scientists who had been gathered to study the Foretold. The dining car revealed itself to be a white laboratory as Gus halted the train and revealed that the whole scenario was set up in order to find out more information about the Foretold.
After several deaths aboard the train, the Doctor explained the mummy to be a soldier, waiting to be dismissed from his duties. After dismissing the Foretold, the mummy disintegrated; its war finally ending. The Doctor rescued all living parties from the train with an improvised teleporter, beaming them into his TARDIS. After the Doctor got inside the TARDIS and attempted to hack Gus to find out who set up the gathering, Gus set off a failsafe, blowing up the Orient Express. (TV: Mummy on the Orient Express)
The Orient Express was included in a series of notes written by Clara when she was planning to confess to Danny Pink via phone call about her adventures with the Doctor. (TV: Dark Water)