... and most of Dunkelzahn's Will had plenty of carrots like Plot #3, and several sticks like Plot #1. So the idea isn't totally new.
What you might do is build up to it - make Mr. Johnson a well-liked and -respected member of the shadow community. Make him someone with fingers in lots of pies, but who did his best to a) do good by his teams, including the PCs, and ) do good by the community. Someone similar to Bull, for example. Not always a totally righteous dude, but a good guy to work for.
Start setting this up early on, if you can - make him a frequent Johnson (1 run in 3, perhaps) or the team's Fixer, let the PCs meet other shadowrunners as both competition and allies when arriving early for a meet or leaving one, or even just standing guard for the guy for a couple days while he does business. (Ooo - I like this latter part. Anyhow.) Start quietly planting hints and implications - this guy has big personal plans, or has a cause he's either the driving force behind or to which he is really dedicated. This makes him enemies, but he's a smart guy, so he has contingency plans in place, and has figured out the 'road signs' on the way to the completion of his goal(s).
Then he gets whacked.
So his assistant (beautiful elf fem or brooding ork, whatever) calls all his teams - the PCs, sure, but you know, a dozen, two dozen other crews from relative noobs with only 3 runs and 20 karma under their belts to street-legend pros who the PCs have only heard about (good time to bring out one or two of those favorite old PCs of your own) and gets them all together. "I regret to inform you all that Johnson X is dead. He has, however, made some plans, and here he is to tell you about it ..."
Then run with all your ideas. Recover the body; identify who did it; take retribution in a truly spectacular and excessive fashion (or subtle and quiet, if you want). Then start pulling out the 'road map requests'. The assistant has the full set of plans, but certain branches are trimmed depending on what happens since the guy's death - the Yakuza are getting uppity, or the Governor is backing down on something, whatever. And the guy has put aside a Big Chunk of Change in order to get all these things done. Oh, there's some room for negotiation - 5k or 10k per entire run (not per runner) at the most, though, so you can start treating them as 'good karma' runs.
Maybe some of the other teams will try to horn in on your PCs' business; ideally, they won't, but that's up to you as the GM. However, sometimes the PCs might be called in with another team, for one or the other of them to act as a distraction - or even both teams mixing, the 'hot members' going off to do the distraction while the 'cool' members do the sneak-and-grab. This could allow the players to design and play other character concepts for single runs, all of them working together on a temporary secure WAN, each player playing two PCs - their own on one team, and a temp one on the other. And you can switch back and forth between tense sneaking and hacking over here and wild heavy-weapons-fire chaos over there.
Or maybe one of the teams does start trying to horn in on the others' jobs, and as a result the PCs are asked to perform an 'overwatch' function for a couple of critical runs by the other teams - and to finalize the troublemakers if they show.
And once The Goal is achieved, you can conclude the adventure series, perhaps with the assistant now taking the old Johnson's job.