In the last session, my runners finally figured out that Mr. Johnson's property had been taken to an Aztechnology research facility.
Their response? Call Mr. Johnson directly and tell him they aren't going to finish the run unless they get paid more!

I rolled with it, and had Mr. Johnson agree to pay them more, but I'm still working out the proper fallout.
Some ideas I've had in mind run along these lines:
- Have Mr. Johnson call the team's Fixer to offer him "his additional cut", have the fixer get really pissed (-1 Loyalty for the contact for each runner)
- Have the fixer call the runners while they are in the middle of sneaking around the facility ... Oops, did one of you forget to set your commlink on silent?
- Have the fixer yell at the characters via commlink while the guards are shooting/casting at them (distraction penalties to dice pools for that combat)
- If the runners don't make good with Mr. Johnson (restore the original rate), they each get a notoriety point.
The player group is not new to role-playing, but they are new to the Shadowrun world.
Truthfully, this Mr. Johnson doesn't have the resources to put the hurt on the team, so they wouldn't have to retire from the shadows.
However, I think I do need some character consequences to drive home the idea: Renegotiating mid-run with the wrong Mr. Johnson is a TERRIBLE idea.
Any other GMs willing to weigh in with ideas or commentary?