I want this to be a big, overarching story, so, taking your advice into account, I'm thinking 7 or 8 runs. Possibly an additional few side runs, that only tangentially tie into the main plot.
The question then is will your players go for that? Make a plot too big, and players will forget why they're even on it by about the sixth or seventh session, even if you keep good records on Obsidian Portal or something. Being generous, maybe half your players will like that, and the rest won't care.
What's more important to most players of any game is knowing that their time at the table isn't wasted. They want something engaging and reactive, that what they're doing is actually leading somewhere. This is why Dungeons and Dragons has lasted so long; no matter what plot you have, as long as you got dungeon maps and treasures and monsters all there, your players will generally stay til the end if they can make it. Puzzles and such also help keep their interest. But if you make things too complicated for them to stay involved in, I assure you unless they're all like the Knights of the Dinner Table, they're going to lose interest, and your game dies.
The Key Events idea is mainly for you to keep things loose enough so that your players will not necessarily follow exactly what you want them to do to resolve the event.
Run 1: From what I recall, in one of the sourcebooks, there was an area in the Barrens called 'the plastic Jungle' (basically a bunch of old greenhouses) where several barrens people had started growing food for themselves and set up a community. My idea is that they are trying to sell their organic food (super pricey since it's not all soy) to the larger world, and the PC's Fixer has set it up for them. The PCs are hired to fend off local gangs while the co-op gets their defenses running. PCs get to know the Co-op. Befriend them?
Run 2?: Another run for the Co-op, just to re-enforce the connection. Probably something like defending the first shipment out of the barrens from more gangers. Try to make the Co-Op likable. Also set up the fact that the runners may be their go-to shippers, so that more money-driven PCs will think they can have a steady stream of cash.
Run 3 (end of run 2?): This is the troubling part. I need the Co-Op to get gunned down, by 'mysterious soldiers.' I could, of course have them see footage of it, but there's something more visceral about being there. Of course, then there's the problem of the PCs pulling a Leroy Jenkins and getting killed trying to take down a clearly superior force. (or some super combat OP character just owning the lot of them.) Any suggestions?
In my opinion, then, you should offer missions on a small-time basis. The first run should be cheap, easy, enough to both introduce who the co-op is for the players with not a whole lot of risk of death (of course, anything could happen). Then, back off for a couple of weeks, and offer the second run along with other runs so that your players don't catch on that you've got a whole campaign set up for this. Try to make it seem they've got control while they're playing in your sandbox. If they refuse that run for whatever reason, fine. Wait a week or so, and offer it again for the same amount of money (they can negotiate, of course, for better pay).
When the co-op gets gunned down, don't have it be part of a run. Make it something that happens. The PCs don't have to be there. Have a survivor hire them. Don't be afraid of the PCs doing legwork, like the Hacker looking up information on any available AR system in the area, or the Mage getting background auras and such. The survivor can fill them in on details, and maybe you can drop a clue at the massacre sight. The Hacker could also try to infiltrate the cops to find out what they know (if any cops decided to investigate the shooting in one of the most dangerous parts of town).
During either the first two runs, the PCs could gain a contact from the co-op. You don't have to have that guy be the survivor. In fact, it might be dramatic if the contact is killed (players get emotionally attached to contacts, in my experience).
Always consider what happens if the PCs just don't give a damn. What happens next? What's the corp's next move? The world goes on even if the players don't do anything.
In my advice of breaking this down into Key Events, the first Key Event could be introduction of the co-op. Second KE is getting a contact. Third is the massacre. Fourth could be a link to whoever did this - maybe they're mercs? Fifth could be determining who hired them. Sixth could be a link to why they massacred these people, perhaps throwing a red herring in here. Seventh is finding out where these skillwires are coming from. Eighth....well, what next? Why would they go to where these skillwires are coming from, and what would they hope to gain from it?
If the Players kill the guys who killed their clients, then likely they may end the investigation there. That's alright! Let them. Then you can re-introduce those skillwires somewhere else.
Remember if you make it too big and then try to dump it all on them, and lead them by the nose, they probably will be turned off. You might even scare them; after all, if they're barren-runners, this might be too big for them to handle. Just take it easy, and let it manifest naturally.
