Krieghund

How about during the mission the player recieves a clue that explains the decision they need to take and which missions they should run depending on the choice they make.

Something like, "You get the magic floppy disk. If you wish to give it to Bob run mission 1234. If you wish to give it to Steve run mission 4321.

Great idea, but the biggest problem you're going to run into is the limit of only being able to have 3 missions published at a time.