Andy's Brief Intro to Story Composing:
Part 1: Introduction.
The protagonists are called to the adventure, and begin preparations, In SR, this is usually when the team meets the Johnson, gets the mission, and starts doing their legwork. This is a good spot to introduce the antagonist - maybe not in person, but through cat's paws, like thugs out to harass and intimidate them. The first problems (e.g. , the lack of the boat) should not be too challenging to accomplish.
Part 2: The Development / The Buildup
The protagonists actually embark on the adventure. This may include more advanced preparations, following up on the first clues, travel to the mission site, or the beginning of the run itself. The team will face increasingly powerful opposition, and start uncovering clues to what is really going on. It's called The Buildup because it builds up dramatic tension that gets resolved in the next part
Part 3: The Climax
This is the most action-packed part of the adventure, when the protagonists realize What Exactly Is Going On, or face down the Big Bad. Usually marked by a sudden change of pace and mood. Several climaxes are possible per story - you alternate between buildup and climax, each time building up more and more tension until the Grand Finalle. E.g., the multi-climax run may have the fight with the Big Bad, the escape and chase scene, and the double-cross by the Johnson. One cool thing to do is make the players feel they've taken down something bigger than them, and barely escaped with their lives. Hard to do, but you should see the high-fives when it's done right.
Part 4: The Aftermath.
The heroes either return to receive their just reward, or lay low and let the heart die down, or ride off into the sunset. A SR classic Johnson Doublecross can be played as a false aftermath, building up to the final climax and the true aftermath after that.
GM's Job:
Start with the story you want to tell. It can be "Corps are evil", "Magic is cool", "Matrix is even cooler", or just "I had MichaelBay-O's for breakfast and want to see stuff blowing up". Develop on that.
Figure out the protagonists' motivation, even if it's just "We want to complete Johnson's mission".
Create a suitable antagonist(s) to challenge the protagonists. Give him a motivation too - even if it's "I want to take over the word just for the heck of it."
Think on how can the protagonists accomplish their goal / thwart the villain's plans. Figure out what obstacles can the antagonist throw at them.
For each obstacle, figure out the likely ways to overcome them (and whether the antagonist thought of that too). Think on what help the protagonists may need - introduce plot devices and secondary characters as necessary.
Figure out the motivations for each secondary character. They will not help the protagonists just like that, each will have their own reasons to do so - money, revenge, or just plain goodness of the heart.
Be prepared for the players to thwart your plans. Improvise as necessary.