Originally, it was believed that the presidential train was a hat placed upon an NPC who had their speed set to abnormally fast and would run along a set path, thus giving the appearance of a working train system. However, the sleuths at PCGamer have dug a little deeper.
The truth is even stranger still: the train is in fact an armor piece that replaces the player character’s right hand entirely and gives the impression the player is inside a train. This also means it isn’t an NPC that powers the train, it’s the player themselves. A unique camera animation then plays along the track the ‘train’ takes.
Running the animation in GECK, Fallout 3’s editor, shows the train and player character to flip sideways, which is odd as it definitely doesn’t happen in-game. Nevertheless, an ingenious solution which most likely saved Bethesda a lot of time.