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TLDR: She gets on the wrong train and through her actions it stops. As she discovers it's the wrong train, it turns out that the right train has come down the tracks behind it and must stop. [Here...
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#3: Attribution notice added
Source: https://writers.stackexchange.com/a/45474 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
TLDR: She gets on the wrong train and through her actions it stops. As she discovers it's the wrong train, it turns out that the right train has come down the tracks behind it and must stop. [Here's my original, probably-too-much-detail answer...] How about, the heroine is tricked by the bad guy and boards the wrong train, sure that it is the correct train. After a series of adventures she manages to get into the engine, locking everyone else out. Unfortunately, modern trains are way more complicated than she thought, and instead of stopping the train she ends up accelerating the train to dangerous speeds, roaring through crossings and switches, causing accidents that destroy some of the railroad infrastructure. The engineer and a railroad security guard are trying to break into the engine to stop the train, and she frustrates them in various ways, while desperately trying to figure out how to stop the train. They have lost contact with central control (due to the infrastructure destruction) and after some random switches don't know where they are. Cut to the target train where the bad guy is smug about his security has worked perfectly and no one knows the actual train he's on. Cut to the heroine, where the engineer and security officer finally break into the engine and stop the train. As it comes to a stop, she sneaks out of the engine and starts running, to get away from her mostly-failed mission. Just then, the real train with the bad guy comes around the bend and sees the now-stopped train directly in front of them. They slam on the brakes and the bad guy assumes that somehow the heroine figured out the correct train and has succeeded in stopping it, so begins to escape the train. The train comes to a halt inches away from the stopped train, and the bad guy jumps off of the train and lands at the feet of the police who are searching for the "terrorist" who hijacked the other train. They recognize the bad guy and take him away, leaving his McGuffin behind for the heroine to pick up.