Drivethrough RPG is also a good source for Shadowrun. They adventure aren't as adaptable (though some might work). I was more just speaking to the planning of contingencies.
It's a lot easier if you write your segment and then at the end go back and ask "OK, I'm assuming they'll take the droid with them... what if they don't?" and go ahead and knock out a paragraph for that. Then if they do decide to leave the droid, you already know what to do to keep the story moving in the right direction.
Like I said, think of the good CoD games like the first Modern Warfare. Each level is in essence just a long hallway that's so well decorated, scripted, and player-focused you don't realize it (at least not on the first playthrough) A good RPG adventure will be a similar thing. While there will be more freedom to decide how to proceed, the goals, obvious available options, and consequences, should always be clear and in the front of the players mind. They'll still go off the rails, but instead of completely going bonkers, they'll just think of a different way to accomplish the goal you already wanted them to accomplish, so improvising on your end won't be so hard.
Getting this down will also open up more complex play and story options once you've got the experience. Imagine a campaign where one of the players is a double agent actually working for the Empire. Trying to just open world sandox that will probably end up with one player thinking his job is to sabotage the rest of the group and generally make a mule out of himself. A structured campaign will allow the GM to give specific secret goals to the spy that will allow him to tag certain plot points in each adventure, so when you reach the end of the campaign and he's revealed as a double agent it'll not only be a surprise, but also all the little details will fall into place (OMG! That's why he went off to repair the ship at that moment on Theferon, because he KNEW the Imperial fleet was about to arrive and he wanted to make sure we escaped with the senator and went on a wild goose chase and kept him from making his address! It was all part of the Emperors plan!)