by some odd coinsidence I'm thinking of Back to the Future II, but that's just me... though it was a good movie..

Anyway, it really does sound like a very strange thing. I've read alternative endings to the same story, but outright alternative chapters is a new one. What could happen to your agents, is that they just took the wrong turn, and now they need to back-track, and follow the right words.

If you imagine the words suddenly splitting up into the odd chapter, and the rest of the story, much like a road splitting up into a road to a dead-end swamp and a road to a glorious field, you could say, your agents just took a wrong turn in reading the words.

This is just a thought I have... but having a loop like Meta suggested could be fun aswell, and yes, see if you can't kill of the Alt!Sue before the story goes on. The more killing the better... I'm sorry, did I say that out loud?

I'd go with the action happening, and then have a sudden wierd temporal/causal loop suddenly flinging the agents back into the main bulk of the fic. You could even have fun with having to kill the Alt!Sue as well if you had the time.

This seems like a massive Big Lipped Alligator moment to me. Maybe the scene happens and then the fanfic just goes on like it would've without that scene in there, thus leaving two very confused agents?