When I get a new group, the first few adventures tend to be things I've designed with a blank template in mind ... the group will have a sammi, a mage, a face, an NPC decker, and so aren't exactly taiolred to a group's unique flavors. After a month, when I know the group isn't breaking up, but the membership has shaken out a tad, and I know who the characters are, that's when the Work starts.
One of the biggest changes in my GM style came from the Buffy RPG, of all things, where they introduced the idea of seasons. I'd always had some story arcs, where adventures would link from one to another, but the seasonal arc allowed me to plan, say, a dozen adventures out in advance, and knowing which ones were where "Metaplot" arcs would hit and where "one-off" arcs would be. I could have some slow stuff and some fast stuff picked and placed, some RP-focused character stuff and some plot-based stuff, and so on. Getting that balance right is tricky, but neat.
So, an arc might look roughly like this.
1 - Cakewalk. The runners are hired by a "Mrs Smith", a client who doesn't have a Johnson, to do a milk run on his own research facility. Job's an easy one ... get in, get a certain McGuffin from a secure lockup, hide it in his workstation, take a few other things to disguise what's really being taken, and beat feet. Low on cash, he lets them steal his car on top of a small payout. The job's crazy easy, no betrayals, and it goes smoothly.
2 - Just a datasteal. Johnson wants a file stolen, the back-up data erased, and a bonus if they can snag a prototype. By-the-numbers run.
3 - Favor for a friend - Someone's contact has a problem. The team bails them out. Low payout, but a good RP session with a karma bonus for everyone.
4 - Something magical. A spirit flips out and kills someone. The group's hired to capture it, but things go sideways and they wind up having to kill it instead. Johnson is grumbly, but still pays out a (lesser) fee. Unknown to them, it ties in to the first McGuffin.
5 - "What do you mean, we aren't hired?" Another RP session with side benefits ... they talk to a Johnson and don't get hired; a rival team does. With time off, they start sniffing around their contacts more, having three low-no payouts in a row. A good time to focus on someone who took on of Those quirks, like Amnesia, or Enemies.
6 - "Hey, it's Doctor Pete!" ... the team is hired to break into a research area and pluck a researcher... the scientist from the first mission! His value must have really gone up! And boy does it, as the Johnson is offering more than usual rates, but insists that the target be extracted with his research and family. Gonna be a hard one. The team's lean and hungry, so dives in. After plucking their old pal, he gives them a counter-offer ... big money to let him go. He doesn't think the extracting corp will let him do what he needs. The team knows he's virtually broke from the last time... do they turn him over or let him go?
7 - Gangers. Shoot them a lot. A straight mission with low moral quandries after the last one. Let the ones who bought new toys show off and blow things up. Everybody needs the release. Nice place to seed things for later.
8 - B&E ... with a twist. The facility is under water, or they need to crack into a blimp that hovers over the city, or a secret R&D facility's in the sewers. Just a little mix-up for when they get cocky. Let them win the contract over the team that got a job over them back in session five.
9 - Johnson with a twist. High time for a Matrix-only Johnson and a mission that's a little odd. Run around and do a bunch of minor things that seem unconnected. In the process, dribble in some stuff that's come up before ... maybe a surviving ganger from before's gotten rebuilt and has a mad-on for them. Maybe another contact is involved in a mission. Just some fun. Drop some clues about the weird spirit issue from way back.
10 - Normal mission to take advantage of a PC ... the team rigger sad that you haven't had a car chase? The samurai reallyneeding a katana-weilding bad guy to duel? The mage getting cocky? Pick one PC who hasn't had a good focus eipsode yet and build the thing to showcase them. EVeryone needs a starring role once!
11 - Big Finale, Part 1. Turns out that Dr Pete's slipped his handlers and gone underground. It also turns out that his research is a Big Deal, and now people are crawling out of teh woodwork looking for him. The PCs have an edge in that they've dealt with him (twice!) and have a head start, but might have to do some digging. (Bet his car has some info. But we sold it! Crud, gotta go track it down!) ... you can start throwing things around, here. RIval team needs to bump into the PCs at least once, and clearly are on the same hunt. Contacts help out, or show up hurt from others beating the bushes. What the heck is the McGuffin that people are so hot for it? And then they find out. Ooohhh crap.
12 - Big Finale, Part 2. Stuff blows up! Guns! Spirits! Oh Em Gee! McGuffin winds up broken and/or Dr Pete winds up dead ... or "dead" and thankful for the team for getting him away from the heat. Team gets a windfall... maybe cash, maybe karma, dependning. Everyone figures out how older adventures linked to this one and go, "Aw man, if we would have ... dude!" Bask in a job well done! Take a week off for everyone to decompress, then get ready for season two.
(A real season would have more detail, obviously, but.)