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One trope reversal would be to short-circuit the whole thing, as Indiana Jones did shooting his exotic weapon duel opponent in the first Raiders movie, or Bourne Identity: girl just goes and asks for the information instead of doing the complicated heist. You expect a big action scene then suddenly nothing. Or Deadpool accidently leaving his guns in the taxi before the big fight.

For instance, maybe she's prepared to blow the track to stop the train. But she has diarrhea and rushes back to a shop to use the toilet and for some reason there's a long line? So she's nervous as heck about the caper and about to explode physically and has to stand in line listening to stupid conversations?

Then, maybe she comes out of the toilet and the train's just happened to stop right there because the driver had a heart attack or something and released the dead man's switch?

Or the toilet was "customers only" so she bought a milkshake she didn't want, and just threw off into the distance as she was returning to her explosives and her weapon/tool stash... and the milkshake coincidently hits the exact train's windshield, blinding the driver whose wipers can't deal with it and has to stop short of the actual trap?

Maybe some minor character she was mean to earlier in the book throws the milkshake at her, resulting in same splat?

Whatever happened, now the train's stopped but not where she planned, and she doesn't have her guns or what have you and has to improvise. Meanwhile the thrower of the milkshake, or maybe a waiter she didn't pay at the restaurant, also follows her onto the train to berate her. She's trying to pay him to get him to leave her alone so she can concentrate on the heist, but no, with him it's a point of honor, and it turns out she doesn't have the right currency, or not enough money anyway. Maybe the reason to stop the train was a maguffin, and the only purpose was to draw these two back together?

Meanwhile make a little point about how her explosives maxed out her credit cards, have her realize she won't be able to afford the minimum monthly payment, etc., then turned out not to even be needed. In the trailing credits or postscript have a scene of her returning the unused explosives and can't get cash back, just store credit. At an explosives dealer. Which sets you up for the sequel...

Probably all a horrible fit for your story but an entertaining break from my work.

The way I understand your conundrum is that you are trying to fit a puckish rogue into an action sequence. It feels out of place likely because it is. I surmise the problem isn't train robbery tropes, it's action tropes. The reason I say that is you mention a guile heroine, and I imagine someone using mind over matter. I don't think a very trope-y action climax really highlights that kind of character, and maybe that's why it doesn't feel right to you.

Take a moment to challenge your own premise. Do you need a moving train? Or a train? Or any vehicle? Why an action sequence instead of a simple caper? I assume you got to "I'm robbing a moving train" for a reason, but by challenging these reasons you might find a different path to the same end result, one that fits your character and story better.

I can't really tell what works and what doesn't without knowing the full story, but you can.

Working with the idea of a train robbery, there are many ways you can put a spin on it. Trains get delayed, or cancelled. It's possible the best place to climb onboard has loads of other trains one can mistake for the target. You can wait for the train to go back to the depot or to a maintenance facility. Or maybe you aren't stealing something on the train, you're stealing the train. Or a wagon at least. That would certainly be less conventional.

I don't know about subverting train robbery tropes, but you can certainly subvert the ending of your train sequence. They climbed on board, fought their way through, only to find out it's an ambush. They'll be taken as prisoners, inside the fortress that hold the McGuffin. Maybe that was even the plan all along. Or at least, that's what your protagonist would claim. Maybe the darned thing that's supervaluable is actually only valuable to its owner and no one else. Or they pick the golden cup when it was the wooden one. Or the treasure was inside of us all along and it really was about the friendships we made along the way.

You mention the character

over-inflates intrigue, misreads clues

Maybe the train isn't a fullscale train but the model train in the bad guy's office. She knew the treasure was inside the train, she just had the wrong idea of which train it was. That would be misreading clues, wouldn't it?

Random thoughts

• The old disconnect the cars trick, but the protagonist is on the wrong section. They see their objective slowing down and dropping away from them as they speed off.
  Realizing they can't just jump, they disconnect another section of train. But the train is now on a flat plain and the first section was on a hill. Now they've stopped, but their objective is coming down the hill at them! (vary the speed according to plot armor).


• Protag boards the train and finally has the dramatic confrontation with their nemesis, just as the train goes into a long tunnel. Overly dramatic lines are punctuated with awkward "I'm over here" statements etc.


• Juxtapose "dramatic train heist" with "boring commute" and the monotony of actual train travel. Board the train with flair and then spend four hours reading the same magazine while you wait for the train to reach junction x.


• Protag chases the train. Villain snarls at engineer to make her go faster. Engineer protests that it can't go any faster or it'll blow. It blows. The train rolls to a stop.


• There are people stuck on the tracks! The protag has to make the heart rending choice between saving their own child's life or killing a whole class of irritating armchair philosophers.

You didn't say whether the train itself has to be a train. That is, maybe one or more of the following design points of a "train" could be subverted:

• The heroine has to perform the heist on a specific train (thanks @Amadeus for highlighting this one!). If that train goes by un-heisted, the heist has failed. ...Or has it?




• Trains move on fixed courses and schedules. Our heroine knows exactly where the train is going to be, and when; and where it's going after that; and exactly how much time she has to perform each stage of the heist. ...Or does she?




• Trains are fragile. If the train is derailed, everyone on board stands a good chance of dying. (This is why historically "train derailment" is up there with "treason" as a capital crime.) Even going around a curve too fast might be enough to wreck the train. The heroine must take precautions to make sure the train remains controlled at all times. ...Or must she?




• Trains are deadly juggernauts. Vice versa, if a train hits someone on the tracks, it'll kill them. For both this reason and the preceding one, the engineer will be on the lookout for people or obstacles ahead, and if there's someone on the tracks or trying to flag down the train, the engineer will stop the train. ...Or will he?




• Trains are long. The heroine might be messing around in the baggage car for several minutes before anyone notices. For either the heroine or her antagonist to get from the front of the train to the back of the train will also take several minutes. ...Or will it?




• Similar to the above: trains are linear. If you're trying to get from the caboose to the engine, and I'm in the middle, you have to go through me. ...Or do you?

Linearity is already popularly subverted via the "heroine runs along the roof of the train" trope. I've never seen "heroine crawls along the bottom of the train" (probably for good reason) or "heroine moves sideways onto a train passing parallel to this one and then moves back." I've also never seen "train is really a big circle with no start or end so there are two ways to get anywhere" or "train is really two-dimensional" (cars spammed out either horizontally or vertically, take your pick).

• Trains are easy to navigate. Because they're linear, there's only two exits from each car, and it's never unclear which is the "forward" exit and which is the "rear" exit. ...Or is it?
  

Make the railroad do the heavy lifting

This will sound weird, but the "train heist" tropes you are talking about are predicated on assumptions that are rather inconsistent with how railroads move goods. In particular, freight railroads are basically jumbo package delivery systems, with much more in common with a mail or parcel delivery service than anything else. (Stuff that moves in unit train volumes is an exception to this rule, but not one your protagonist has to trouble herself with.)

With this in mind, we can ask ourselves "why go through all the pain of trying to rob the delivery truck, when your protagonist can simply get their quarry delivered to their proverbial doorstep instead?" Your description of them as a "guile heroine" sounds precisely suited to social engineering attacks on the people and systems responsible for determining how cars are routed through the network. Once she gets the system to misroute the target car to her, then she can simply collect the goods in broad daylight, and very few witnesses would be any bit the wiser to what just happened. (Of course, repeating this runs the risk that the lost-car desk catches up to her scheme, as the cars in question would be reported to the railroad's lost-and-found, basically.)

There is also the option of getting the car to be routed as a bad order car, either through physical sabotage (of the target railcar) or information warfare. This has the potential to defeat even the heaviest of armed security due to the dilemma it poses for the crew: either delay the shipment by days to chase a broken-down (or "broken-down") railcar to a shop, or leave the car behind in order to get the rest of the shipment to its destination in a timely fashion.

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.

I'd go with a double (or triple?) con and a play showing you know all about the train heist trope.

If your heroine has an antagonist or someone she needs to get rid of, have her plan the whole train heist with them, and perform it according to the full trope — or perhaps, use other answers here to make the heist less tropey. (Or maybe she could do the heist with just anyone, but I think your effect would be even bigger if it's someone she needs to get rid of.)

However, your heroine is "working undercover" and leads the bad guys into a trap set by the "feds".

And while the bad guys are being arrested, your heroine steals the package or whatever you want to heist, preferably something other than the target of the original heist (diamonds instead of gold bars, info instead of guns, etc... something "lighter" and "smarter").

And only later do the feds realize that dependable agent from agency X is gone and oops agency X has no clue who that is... and where is the McGuffin! Crap!

Done right you hint at different layers of the final con during the story. Perhaps a meeting with a buyer for the McGuffin stolen in the end. Perhaps your heroine purchasing false credentials (maybe even as "an agent of Agency X" — you'll have to feel out how much you can reveal).

I think this one done a bit badly would be with flashbacks that reveal key clues as the con unravels layer by layer. (And that may be a must to make it work...)

Or the story could jump back and forth between the heist and what your heroine does to set it up before it happens. Maybe even starting with the heist, doing a bit of it, jumping back, then doing a little bit more, and jump back to reveal even more of what happened before.

The classic in media res start is to do the heist until it seems to get really bad and then jump back to "4 days earlier". However, I think that one works best on TV, several episodes into the show, when we already know and care for the characters.

Just writing the heist scenes knowing there's a second and third con going on might give the reader a feeling something isn't right with the heist, but you could plant hints on purpose as well to give that, something-is-up feeling.

Don't touch the train itself

This might not be what you're looking for, but something to consider anyway.

Remember that a train isn't an autonomous vehicle controlled by the driver alone. So have the action take place in a signal box and/or signalling control centre. The MC can fight for control of signalling and switching; this fight could be physical, psychological or even cybercriminal, depending on the story setting.

For an example of this approach (though planned, heist-style, rather than haphazard as your MC seems to be), I recommend viewing The Train (1964). The early parts involve taking control of the train via its control structure, and it later switches to the conventional form of the trope, with fighting on and around the vehicle itself.

I'd like to see the heroine make a case to the train conductor that the crew is badly treated by their employer and should go on strike ... immediately.

Of course, it might be a bit too realistic for readers in certain countries.

Stripped of all the self-aware, meta jargon, the problem is that your hero isn't well suited to a big, action-packed showdown --she's more likely to win with her wits than her fists. Given that, I'd lead the reader to expect the big, action packed showdown, allow her to be physically overpowered, and only then reveal that she's already anticipated this outcome, and secretly solved it in advance using her wits. (Bonus points if her physical defeat is an essential part of her ultimate strategic victory!) The Sting is a good example of this kind of reversal. You'll have to work hard, however, if you want to play fair with your readers on this one --The Sting is only semi-successful from that point of view.

"What the --? The train is stopping? But that's impossible."

"Not at all. You see, you were fighting to win. I was fighting to keep you distracted."

The reason this should work is that you've done the work to establish your hero as a master strategist. So the seeming action ending will seem like a cheat to the reader --as indeed it did to you, the author. Then when you reveal the action ending was just a sham, it should feel right to the reader, in a very satisfying way, if you've done the work.

Heroine plans big heist...then sees cargo unattended prior to being boarded on train, so makes off with it before the train leaves the station.

Or heroine does this, but still needs to get to the train's destination, so has to board the train with the cargo, but the nature of the cargo makes this hard to do without being caught.

Or the heroine secures the item before the train leaves, but the heist is a trick she is playing on her supposed colleagues.

Or the heist is a dodge; she doesn't care about the item to be stolen, but she does need to smuggle herself to wherever the train is going. Maybe she's like to foil the heist if she could, without being caught herself.

Like most action stories, the train heist is a fantasy of agency, decision, autonomy, and freedom -- this is basis of the appeal of "rule breakers" in all kinds of stories. The audience identifies with the hero/heroine and vicariously enjoys their exercise of will, even if, or especially if, at the expense of others. As most people in most societies are hemmed in by the expectations of others, the simple assertion of me, me, me, me is tremendously exciting. From what I can tell, the most fundamental upending of heist tropes would be to undo the basis of that fantasy.

An example that comes to mind is "Dog Day Afternoon" (bank robbery, not a train) from about 1974. The robbers come in and exercise their free will, but it all unravels quickly because they have no idea what they're doing. "The Taking of Pelham 123" is similar (it's reasonable to consider it a "Dog Day" ripoff) and maybe even "Fargo". The undoing of the action fantasy in "Dog Day Afternoon" can probably be seen in the wider context of the 1970's New Hollywood creative movement against basic motifs and assumptions of earlier filmmaking.

EDIT: On rereading what I wrote, I was talking about the story as if it were a movie. I don't think anything fundamental changes if the medium is written rather than filmed, so I'll just let it stand.

She races to the station to try and board the train, and - it's not there. Where's the train? She waits around for half an hour and the train still doesn't show. Turns out the cops/FBI/DoT/whoever already knew about the danger and stopped the train 3 stations ago...

Have your 'hero' make all of the plans, flesh out the story, buy the supplies, etc but occasionally have something obvious not be available (out of stock on dynamite) and then, right before your hero stops the train (1 mile before) have someone else stop the train for their own nefarious reasons that do not conflict with the hero's reasons such that she is able to ride up, do her stuff and then gets the hell out of dodge less as a hero and more as a parasite.

NB: The reason why, if reflection, so many things she wanted were out of stock were because someone else was doing the same thing as her.

She could first.

1. Buy a ticket


2. Steal a ticket


3. Forge a ticket


4. Get a ticket under another name.


5. If its a steam engine, get on while its refueling water.

After that it depends what she is after.

A shipment of gold.

Sneak back to where the gold is and decouple just the train car with the gold on it. Preferable at night when her activities are harder to see, and more people are a sleep.

The passengers.

1. The pick pocket


2. Knock every one out with a harmless oderless, if possible, gas (chloroform, not odorless). Go through and freely steel their stuff, and leave without any one noticing anything besides being robbed.(of course).

The train.

Use knock out gas in the middle of no where, stop the train yourself.
Drag all the unconscious passengers and staff off the train in the middle of no where. Then leave without them.