I have this idea bouncing in my head of a mission-based CRPG whose missions would be constructed of modules (recruitment, planning/preparation, entry, execution, exit, getting paid) and each would have random variables. It was for Shadowrun originally I guess, so you might find that when you go execute your mission, your target location might be surrounded by a crowd of protestors, or your run might be interrupted by another group coming in to do the same or some other objective at your location, that sort of things. It'd be really tough to balance right, but conceptually not outlandishly difficult to execute, I believe.
(Sorry for the tangent.)
No worries, it's fun stuff to think about 
Hmm. I wonder how it would feel - with a fairly rigid structure like that, it might end up more obviously "X things can happen at these particular points", so not so much emergent stories but randomized content. I mean, if the approach is to implement a set of variations for the specific piece of the sequence, that's at odds with what "emergent" means, right? Which if I had to define quickly would be something like "unexpected but compelling results from the interaction of different rules".
But say the variations in the different pieces were based on some prior events in other missions, all operating based on some set of rules... then it gets more interesting. Yeah, it's fun stuff to think about.
A issue I see is that the connection points between modules have to be rigid to allow exchanging modules. So while what happens during a module can vary, the start and end conditions would always be the same, right? Like in the boardgame Tsuro, you have varied tiles but the connections are all the same.
That does seem like it come become predictable and boring pretty fast.
Yes and no. Things like entry and exit could be incorporated on the same map as generation parameters. (Inside of target building would have its own parameters, as would inside, and entry/exit randomisations might be present on the map from the start or only come into play at a later date. You might see someone already fighting there when you go in, or there might be a power outage during your run, whatever.)
But you are right that giving a sufficient amount of material for the system to create enough variety and still keep the system from becoming too messy to debug would be the biggest problem. If it was just preset modules (entry map A3, entry scenario B3, interior map A5, interior scenario A5, exit scenario A2...), it would be too rigid and become predictable. They'd have to be more along the lines of this:
The target is a city-based research site for a wealthy corp, so there are exterior map modules wealthy_neighbourhood, isolated_zone and high_tech_zone as possibilities. They give modifiers to the map generation algorithm, activity (civilian, police, criminal, miscellaneous, all separate functions that should affect one another) randomisers, entry point generation (you won't find "broken down wall" in a wealthy downtown district unless you've rolled for a heavy attack to be underway when you go in, for example) and so on. Add in chances for effects from past entanglements (you've done a noisy job in this area recently, so any security forces get a bonus to alertness, numbers and equipment, plus there's a chance that AI you *** off may try to trip you up by feeding your opposition damaging info)...
That's the sort of thing I was thinking of. Like I said, it would be a far from trivial coding exercise, but I don't believe it'd be impossible to pull off successfully. But it's not an "oh yeah, maybe add this in too" feature, it'd have to be a central focus.